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From: <sfr...@us...> - 2011-05-19 21:28:23
|
Revision: 878
http://treebase.svn.sourceforge.net/treebase/?rev=878&view=rev
Author: sfrgpiel
Date: 2011-05-19 21:28:17 +0000 (Thu, 19 May 2011)
Log Message:
-----------
Modified Paths:
--------------
trunk/oai-pmh_data_provider/data_provider_web/src/test/resources/jdbc.properties
Modified: trunk/oai-pmh_data_provider/data_provider_web/src/test/resources/jdbc.properties
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/src/test/resources/jdbc.properties 2011-05-19 21:25:28 UTC (rev 877)
+++ trunk/oai-pmh_data_provider/data_provider_web/src/test/resources/jdbc.properties 2011-05-19 21:28:17 UTC (rev 878)
@@ -2,8 +2,8 @@
jdbc.driverClassName=org.postgresql.Driver
jdbc.url=jdbc:postgresql://treebasedb-dev.nescent.org/treebasedev
-jdbc.username=treebase_app
-jdbc.password=tim5tema
+jdbc.username=************
+jdbc.password=********
hibernate.dialect=org.hibernate.dialect.PostgreSQLDialect
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|
|
From: <sfr...@us...> - 2011-05-19 21:25:34
|
Revision: 877
http://treebase.svn.sourceforge.net/treebase/?rev=877&view=rev
Author: sfrgpiel
Date: 2011-05-19 21:25:28 +0000 (Thu, 19 May 2011)
Log Message:
-----------
Modified Paths:
--------------
trunk/oai-pmh_data_provider/data_provider_web/target/test-classes/jdbc.properties
Modified: trunk/oai-pmh_data_provider/data_provider_web/target/test-classes/jdbc.properties
===================================================================
--- trunk/oai-pmh_data_provider/data_provider_web/target/test-classes/jdbc.properties 2011-05-19 17:21:51 UTC (rev 876)
+++ trunk/oai-pmh_data_provider/data_provider_web/target/test-classes/jdbc.properties 2011-05-19 21:25:28 UTC (rev 877)
@@ -2,8 +2,8 @@
jdbc.driverClassName=org.postgresql.Driver
jdbc.url=jdbc:postgresql://treebasedb-dev.nescent.org/treebasedev
-jdbc.username=treebase_app
-jdbc.password=tim5tema
+jdbc.username=************
+jdbc.password=********
hibernate.dialect=org.hibernate.dialect.PostgreSQLDialect
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|
|
From: <hs...@us...> - 2011-05-19 17:21:57
|
Revision: 876
http://treebase.svn.sourceforge.net/treebase/?rev=876&view=rev
Author: hshyket
Date: 2011-05-19 17:21:51 +0000 (Thu, 19 May 2011)
Log Message:
-----------
Fixing Google Analytics code to properly track downloads
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/scripts/googleAnalytics.js
Modified: trunk/treebase-web/src/main/webapp/scripts/googleAnalytics.js
===================================================================
--- trunk/treebase-web/src/main/webapp/scripts/googleAnalytics.js 2011-05-19 14:14:27 UTC (rev 875)
+++ trunk/treebase-web/src/main/webapp/scripts/googleAnalytics.js 2011-05-19 17:21:51 UTC (rev 876)
@@ -25,7 +25,7 @@
if (isDoc) {
startListening(hrefs[l],"click",trackExternalLinks);
}
- } else if (!hrefs[l].href.match(/^javascript:/)) {
+ } else if (hrefs[l].hostname != location.hostname) {
startListening(hrefs[l],"click",trackExternalLinks);
}
}
@@ -46,7 +46,7 @@
function trackMailto (evnt) {
var href = (evnt.srcElement) ? evnt.srcElement.href : this.href;
var mailto = "/mailto/" + href.substring(7);
- if (typeof(pageTracker) == "object") pageTracker._trackPageview(mailto);
+ if (typeof( _gat._getTrackerByName()) == "object") _gat._getTrackerByName()._trackPageview(mailto);
}
function trackExternalLinks (evnt) {
@@ -56,6 +56,6 @@
}
var lnk = (e.pathname.charAt(0) == "/") ? e.pathname : "/" + e.pathname;
if (e.search && e.pathname.indexOf(e.search) == -1) lnk += e.search;
- if (e.hostname != location.host) lnk = "/external/" + e.hostname + lnk;
- if (typeof(pageTracker) == "object") pageTracker._trackPageview(lnk);
+ if (e.hostname != location.hostname) lnk = e.hostname + lnk;
+ if (typeof( _gat._getTrackerByName()) == "object") _gat._getTrackerByName()._trackPageview(lnk);
}
\ No newline at end of file
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|
|
From: <rv...@us...> - 2011-05-19 14:14:34
|
Revision: 875
http://treebase.svn.sourceforge.net/treebase/?rev=875&view=rev
Author: rvos
Date: 2011-05-19 14:14:27 +0000 (Thu, 19 May 2011)
Log Message:
-----------
targetCount == 0 for the root node, assuming that the edges array does not include the root edge.
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/scripts/jsphylosvg-min.js
Modified: trunk/treebase-web/src/main/webapp/scripts/jsphylosvg-min.js
===================================================================
--- trunk/treebase-web/src/main/webapp/scripts/jsphylosvg-min.js 2011-05-19 13:31:28 UTC (rev 874)
+++ trunk/treebase-web/src/main/webapp/scripts/jsphylosvg-min.js 2011-05-19 14:14:27 UTC (rev 875)
@@ -757,7 +757,7 @@
// RAV: it is more robust to search for the root by the tree topology
// then by looking for a @root attribute. Valid NeXML tree structures
- // always have one node with fewer than 2 edges pointing into it. The
+ // always have one node without normal edges pointing into it. The
// root attribute is used to indicate that this tree is actually rooted.
// Compare this with nexus/newick: newick strings are always implicitly
// rooted, even if the tree is called a utree or the [&U] token is used.
@@ -769,7 +769,7 @@
targetCount++;
}
}
- if ( targetCount < 2 ) {
+ if ( targetCount == 0 ) {
root = nexNodes[i];
}
}
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|
|
From: <rv...@us...> - 2011-05-19 13:31:37
|
Revision: 874
http://treebase.svn.sourceforge.net/treebase/?rev=874&view=rev
Author: rvos
Date: 2011-05-19 13:31:28 +0000 (Thu, 19 May 2011)
Log Message:
-----------
Root is now found by looking at the topology instead of searching for a @root attribute.
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/scripts/jsphylosvg-min.js
Modified: trunk/treebase-web/src/main/webapp/scripts/jsphylosvg-min.js
===================================================================
--- trunk/treebase-web/src/main/webapp/scripts/jsphylosvg-min.js 2011-05-19 13:00:28 UTC (rev 873)
+++ trunk/treebase-web/src/main/webapp/scripts/jsphylosvg-min.js 2011-05-19 13:31:28 UTC (rev 874)
@@ -755,20 +755,13 @@
nexNodes = jsonString.trees[0].tree[0].node;
}
+ // RAV: it is more robust to search for the root by the tree topology
+ // then by looking for a @root attribute. Valid NeXML tree structures
+ // always have one node with fewer than 2 edges pointing into it. The
+ // root attribute is used to indicate that this tree is actually rooted.
+ // Compare this with nexus/newick: newick strings are always implicitly
+ // rooted, even if the tree is called a utree or the [&U] token is used.
for(i = 0; i < nexNodes.length; i++){
- if(nexNodes[i].root && nexNodes[i].root == "true"){
- root = nexNodes[i];
- }
- }
-
- // RAV: the root attribute is used to indicate whether an implicitly rooted
- // topology should, from a biological p.o.v., be considered as such. However,
- // valid NeXML tree structures are always rooted, even if they don't have
- // the root attribute, in the sense that there's always going to be one node
- // that doesn't have two edges pointing into it. It seems to me that we can
- // still render these trees, we just have to find which node is the one that
- // doesn't have two edges pointing in. This loop does that.
- if (!root){
for(i = 0; i < nexNodes.length; i++) {
var targetCount = 0;
for(j = 0; j < nexEdges.length; j++) {
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|
|
From: <rv...@us...> - 2011-05-19 13:00:35
|
Revision: 873
http://treebase.svn.sourceforge.net/treebase/?rev=873&view=rev
Author: rvos
Date: 2011-05-19 13:00:28 +0000 (Thu, 19 May 2011)
Log Message:
-----------
Added additional loop to identify the root node based on the implicit topology (instead of by looking for the @root attribute).
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/scripts/jsphylosvg-min.js
Modified: trunk/treebase-web/src/main/webapp/scripts/jsphylosvg-min.js
===================================================================
--- trunk/treebase-web/src/main/webapp/scripts/jsphylosvg-min.js 2011-05-19 12:57:49 UTC (rev 872)
+++ trunk/treebase-web/src/main/webapp/scripts/jsphylosvg-min.js 2011-05-19 13:00:28 UTC (rev 873)
@@ -761,6 +761,27 @@
}
}
+ // RAV: the root attribute is used to indicate whether an implicitly rooted
+ // topology should, from a biological p.o.v., be considered as such. However,
+ // valid NeXML tree structures are always rooted, even if they don't have
+ // the root attribute, in the sense that there's always going to be one node
+ // that doesn't have two edges pointing into it. It seems to me that we can
+ // still render these trees, we just have to find which node is the one that
+ // doesn't have two edges pointing in. This loop does that.
+ if (!root){
+ for(i = 0; i < nexNodes.length; i++) {
+ var targetCount = 0;
+ for(j = 0; j < nexEdges.length; j++) {
+ if(nexEdges[j].target == nexNodes[i].id) {
+ targetCount++;
+ }
+ }
+ if ( targetCount < 2 ) {
+ root = nexNodes[i];
+ }
+ }
+ }
+
if(root){
root = recursiveParse(root);
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|
|
From: <rv...@us...> - 2011-05-19 12:57:55
|
Revision: 872
http://treebase.svn.sourceforge.net/treebase/?rev=872&view=rev
Author: rvos
Date: 2011-05-19 12:57:49 +0000 (Thu, 19 May 2011)
Log Message:
-----------
In rooted trees the root attribute needs to be set on the node it applies to. Omitting the attribute caused jsPhyloSVG to complain.
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlTreeBlockConverter.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlTreeBlockConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlTreeBlockConverter.java 2011-05-17 21:03:38 UTC (rev 871)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlTreeBlockConverter.java 2011-05-19 12:57:49 UTC (rev 872)
@@ -3,7 +3,6 @@
import java.util.Iterator;
import java.util.Set;
-import org.cipres.treebase.Constants;
import org.cipres.treebase.domain.study.Study;
import org.cipres.treebase.domain.taxon.TaxonLabel;
import org.cipres.treebase.domain.taxon.TaxonLabelHome;
@@ -130,6 +129,9 @@
if ( null != tbNode.getName() ) {
xmlNode.setLabel(tbNode.getName());
}
+ if ( tbNode.isRootNode() ) {
+ xmlNode.setRoot(true);
+ }
attachTreeBaseID(xmlNode, tbNode,PhyloTreeNode.class);
TaxonLabel taxonLabel = tbNode.getTaxonLabel();
if ( null != taxonLabel ) {
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|
|
From: SourceForge.net <no...@so...> - 2011-05-18 03:18:11
|
Bugs item #3302986, was opened at 2011-05-16 15:11 Message generated for change (Settings changed) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3302986&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None >Status: Closed Priority: 7 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: hshyket (hshyket) Summary: Study Search crowded with buttons Initial Comment: The study search is crowded with buttons ("Study ID" "Legacy Study ID" "Author" "Title" "Abstract" and "Entire Citation" "All test"). Instead of having separate buttons, could we have a dropdown or popup list for these things plus a "Search" button. This will be especially needed when the prism.publicationDate, prism.modificationDate, and prism.creationDate search terms are introduced (per Revision: 844, http://treebase.svn.sourceforge.net/treebase/?rev=844&view=rev). It would be best if the default item in the dropdown is set to whatever was last used by the user in the session. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3302986&group_id=248804 |
|
From: SourceForge.net <no...@so...> - 2011-05-18 03:16:52
|
Bugs item #3303346, was opened at 2011-05-17 10:30 Message generated for change (Comment added) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3303346&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None >Status: Closed Priority: 9 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: hshyket (hshyket) Summary: Tracking Usage Statistics Initial Comment: We need a mechanism for tracking usage (e.g. how often people search the database, how often a tree, matrix, or analysis is downloaded), possibly collecting other data like IP origin. Finding a solution to for this might be complicated by the fact that we ask robots not to scrape TreeBASE. I put this as a high priority because we need to start collecting this data soon in anticipation of applying for new funding. ---------------------------------------------------------------------- >Comment By: William Piel (sfrgpiel) Date: 2011-05-17 23:16 Message: Tracking is now available through Google Analytics: http://www.google.com/analytics/ If anyone wants access, please contact Harry ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3303346&group_id=248804 |
|
From: <hs...@us...> - 2011-05-17 21:03:45
|
Revision: 871
http://treebase.svn.sourceforge.net/treebase/?rev=871&view=rev
Author: hshyket
Date: 2011-05-17 21:03:38 +0000 (Tue, 17 May 2011)
Log Message:
-----------
Changing search so that there are no longer multiple buttons but a dropdown of the list of options
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchController.java
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/matrixSimpleSearchForm.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/studyKeywordSearchForm.jsp
trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeSimpleSearchForm.jsp
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchController.java 2011-05-17 20:17:26 UTC (rev 870)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/SearchController.java 2011-05-17 21:03:38 UTC (rev 871)
@@ -378,6 +378,7 @@
protected void saveSearchResults(HttpServletRequest request, SearchResults<?> results) {
request.getSession().setAttribute("searchResults", results == null ? null : results.freeze());
request.getSession().setAttribute("searchTerm", request.getParameter("searchTerm"));
+ request.getSession().setAttribute("searchButton", request.getParameter("searchButton"));
}
abstract SearchResultsType currentSearchType() ;
@@ -477,6 +478,17 @@
return matches;
}
+ protected Map<String,Object> referenceData(HttpServletRequest pRequest) throws Exception {
+ LOGGER.info("in referenceData");
+
+ Map<String,Object> resultMap = new HashMap<String,Object>();
+
+ resultMap.put("buttonName", pRequest.getSession().getAttribute("searchButton"));
+
+ return resultMap;
+
+ }
+
public SearchService getSearchService() {
return searchService;
}
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/matrixSimpleSearchForm.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/matrixSimpleSearchForm.jsp 2011-05-17 20:17:26 UTC (rev 870)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/matrixSimpleSearchForm.jsp 2011-05-17 21:03:38 UTC (rev 871)
@@ -1,13 +1,26 @@
<%@ include file="/common/taglibs.jsp"%>
+<%
+ java.util.LinkedHashMap searchOptions = new java.util.LinkedHashMap();
+ searchOptions.put("matrixID", "Matrix ID");
+ searchOptions.put("matrixTitle", "Title");
+ searchOptions.put("matrixType", "Type");
+ searchOptions.put("matrixNTAX", "NTAX");
+ searchOptions.put("matrixNCHAR", "NCHAR");
+
+ pageContext.setAttribute("searchOptions", searchOptions);
+%>
<form id="searchSimple" method="post">
<fieldset>
Search: <input type="hidden" name="formName" value="matrixSimple"/>
<input type=text class="textCell" style="width:150px" name="searchTerm" id="keyword" value="${searchTerm}"/>
- <button type="submit" name="searchButton" value="matrixID">Matrix ID</button>
- <button type="submit" name="searchButton" value="matrixTitle">Title</button>
- <button type="submit" name="searchButton" value="matrixType">Type</button>
- <button type="submit" name="searchButton" value="matrixNTAX">NTAX</button>
- <button type="submit" name="searchButton" value="matrixNCHAR">NCHAR</button>
+ <select name="searchButton">
+ <c:forEach var="options" items="${searchOptions}">
+ <option value="${options.key}" <c:if test="${options.key == searchButton}">selected="selected"</c:if> />
+ ${options.value}
+ </option>
+ </c:forEach>
+ </select>
+ <button type="submit" name="submit" >Search</button>
<a href="#" class="openHelp" onclick="openHelp('matrixSimpleSearchForm')">
<img class="iconButton" src="<fmt:message key="icons.help"/>" />
</a>
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/studyKeywordSearchForm.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/studyKeywordSearchForm.jsp 2011-05-17 20:17:26 UTC (rev 870)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/studyKeywordSearchForm.jsp 2011-05-17 21:03:38 UTC (rev 871)
@@ -1,16 +1,30 @@
<%@ include file="/common/taglibs.jsp"%>
+<%
+ java.util.LinkedHashMap searchOptions = new java.util.LinkedHashMap();
+ searchOptions.put("studyID", "Study ID");
+ searchOptions.put("legacyStudyID", "Legacy Study ID");
+ searchOptions.put("authorKeyword", "Author");
+ searchOptions.put("titleKeyword", "Title");
+ searchOptions.put("abstractKeyword", "Abstract");
+ searchOptions.put("citationKeyword", "Entire citation");
+ searchOptions.put("textKeyword", "All text");
+
+ pageContext.setAttribute("searchOptions", searchOptions);
+
+%>
<form id="searchSimple" method="post">
<fieldset>
For study IDs with values less than 3000, please search using the "Legacy Study ID" button.<br>
Search: <input type="hidden" name="formName" value="searchKeyword"/>
<input type="text" class="textCell" style="width:150px" name="searchTerm" id="keyword" value="${searchTerm}"/>
- <button type="submit" name="searchButton" value="studyID">Study ID</button>
- <button type="submit" name="searchButton" value="legacyStudyID">Legacy Study ID</button>
- <button type="submit" name="searchButton" value="authorKeyword">Author</button>
- <button type="submit" name="searchButton" value="titleKeyword">Title</button>
- <button type="submit" name="searchButton" value="abstractKeyword">Abstract</button>
- <button type="submit" name="searchButton" value="citationKeyword">Entire citation</button>
- <button type="submit" name="searchButton" value="textKeyword">All text</button>
+ <select name="searchButton">
+ <c:forEach var="options" items="${searchOptions}">
+ <option value="${options.key}" <c:if test="${options.key == searchButton}">selected="selected"</c:if> />
+ ${options.value}
+ </option>
+ </c:forEach>
+ </select>
+ <button type="submit" name="submit" >Search</button>
<a href="#" class="openHelp" onclick="openHelp('studyKeywordSearchForm')">
<img class="iconButton" src="<fmt:message key="icons.help"/>" />
</a>
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeSimpleSearchForm.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeSimpleSearchForm.jsp 2011-05-17 20:17:26 UTC (rev 870)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/search/treeSimpleSearchForm.jsp 2011-05-17 21:03:38 UTC (rev 871)
@@ -1,14 +1,27 @@
<%@ include file="/common/taglibs.jsp"%>
+<%
+ java.util.LinkedHashMap searchOptions = new java.util.LinkedHashMap();
+ searchOptions.put("treeID", "Tree ID");
+ searchOptions.put("treeTitle", "Title");
+ searchOptions.put("treeType", "Type");
+ searchOptions.put("treeKind", "Kind");
+ searchOptions.put("treeQuality", "Quality");
+ searchOptions.put("treeNTAX", "NTAX");
+
+ pageContext.setAttribute("searchOptions", searchOptions);
+%>
<form id="searchSimple" method="post">
<fieldset>
Search: <input type="hidden" name="formName" value="treeSimple"/>
<input type="text" class="textCell" style="width:150px" name="searchTerm" id="keyword" value="${searchTerm}"/>
- <button type="submit" name="searchButton" value="treeID">Tree ID</button>
- <button type="submit" name="searchButton" value="treeTitle">Title</button>
- <button type="submit" name="searchButton" value="treeType">Type</button>
- <button type="submit" name="searchButton" value="treeKind">Kind</button>
- <button type="submit" name="searchButton" value="treeQuality">Quality</button>
- <button type="submit" name="searchButton" value="treeNTAX">NTAX</button>
+ <select name="searchButton">
+ <c:forEach var="options" items="${searchOptions}">
+ <option value="${options.key}" <c:if test="${options.key == searchButton}">selected="selected"</c:if> />
+ ${options.value}
+ </option>
+ </c:forEach>
+ </select>
+ <button type="submit" name="submit" >Search</button>
<a href="#" class="openHelp" onclick="openHelp('treeSimpleSearchForm')">
<img class="iconButton" src="<fmt:message key="icons.help"/>" />
</a>
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|
|
From: <hs...@us...> - 2011-05-17 20:17:32
|
Revision: 870
http://treebase.svn.sourceforge.net/treebase/?rev=870&view=rev
Author: hshyket
Date: 2011-05-17 20:17:26 +0000 (Tue, 17 May 2011)
Log Message:
-----------
Adding in Google Analytics tracking functionality
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/decorators/adminTemplate.jsp
trunk/treebase-web/src/main/webapp/decorators/defaultSearchTemplate.jsp
trunk/treebase-web/src/main/webapp/decorators/defaultTemplate.jsp
trunk/treebase-web/src/main/webapp/decorators/mainTemplate.jsp
Added Paths:
-----------
trunk/treebase-web/src/main/webapp/common/googleAnalytics.jsp
trunk/treebase-web/src/main/webapp/scripts/googleAnalytics.js
Added: trunk/treebase-web/src/main/webapp/common/googleAnalytics.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/common/googleAnalytics.jsp (rev 0)
+++ trunk/treebase-web/src/main/webapp/common/googleAnalytics.jsp 2011-05-17 20:17:26 UTC (rev 870)
@@ -0,0 +1,15 @@
+<%@include file="/common/taglibs.jsp" %>
+<script type="text/javascript" src="<c:url value='/scripts/googleAnalytics.js'/>"></script>
+<script type="text/javascript">
+
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-23411098-1']);
+ _gaq.push(['_trackPageview']);
+
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+
+</script>
\ No newline at end of file
Modified: trunk/treebase-web/src/main/webapp/decorators/adminTemplate.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/decorators/adminTemplate.jsp 2011-05-17 19:19:58 UTC (rev 869)
+++ trunk/treebase-web/src/main/webapp/decorators/adminTemplate.jsp 2011-05-17 20:17:26 UTC (rev 870)
@@ -61,6 +61,6 @@
<!-- BEING FOOTER -->
<div id="footer"><c:import url="/common/footer.jsp" /></div>
</div> <!-- END WRAP -->
-
+<jsp:include page="/common/googleAnalytics.jsp"/>
</body>
</html>
\ No newline at end of file
Modified: trunk/treebase-web/src/main/webapp/decorators/defaultSearchTemplate.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/decorators/defaultSearchTemplate.jsp 2011-05-17 19:19:58 UTC (rev 869)
+++ trunk/treebase-web/src/main/webapp/decorators/defaultSearchTemplate.jsp 2011-05-17 20:17:26 UTC (rev 870)
@@ -158,6 +158,6 @@
<!-- BEGIN FOOTER -->
<div id="footer"><c:import url="/common/footer.jsp" /></div>
</div> <!-- END WRAP -->
-
+<jsp:include page="/common/googleAnalytics.jsp"/>
</body>
</html>
\ No newline at end of file
Modified: trunk/treebase-web/src/main/webapp/decorators/defaultTemplate.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/decorators/defaultTemplate.jsp 2011-05-17 19:19:58 UTC (rev 869)
+++ trunk/treebase-web/src/main/webapp/decorators/defaultTemplate.jsp 2011-05-17 20:17:26 UTC (rev 870)
@@ -104,6 +104,6 @@
<!-- BEING FOOTER -->
<div id="footer"><c:import url="/common/footer.jsp" /></div>
</div> <!-- END WRAP -->
-
+<jsp:include page="/common/googleAnalytics.jsp"/>
</body>
</html>
\ No newline at end of file
Modified: trunk/treebase-web/src/main/webapp/decorators/mainTemplate.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/decorators/mainTemplate.jsp 2011-05-17 19:19:58 UTC (rev 869)
+++ trunk/treebase-web/src/main/webapp/decorators/mainTemplate.jsp 2011-05-17 20:17:26 UTC (rev 870)
@@ -28,6 +28,6 @@
<!-- BEING FOOTER -->
<div id="footer"><jsp:include page="/common/footer.jsp"/></div>
</div> <!-- END WRAP -->
-
+<jsp:include page="/common/googleAnalytics.jsp"/>
</body>
</html>
\ No newline at end of file
Added: trunk/treebase-web/src/main/webapp/scripts/googleAnalytics.js
===================================================================
--- trunk/treebase-web/src/main/webapp/scripts/googleAnalytics.js (rev 0)
+++ trunk/treebase-web/src/main/webapp/scripts/googleAnalytics.js 2011-05-17 20:17:26 UTC (rev 870)
@@ -0,0 +1,61 @@
+// This javascript tags file downloads and external links in Google Analytics.
+// You need to be using the Google Analytics New Tracking Code (ga.js)
+// for this script to work.
+// To use, place this file on all pages just above the Google Analytics tracking code.
+// All outbound links and links to non-html files should now be automatically tracked.
+//
+// This script has been provided by Goodwebpractices.com
+// Thanks to ShoreTel, MerryMan and Colm McBarron
+//
+// www.goodwebpractices.com
+// VKI has made changes as indicated below.
+
+if (document.getElementsByTagName) {
+ // Initialize external link handlers
+ var hrefs = document.getElementsByTagName("a");
+ for (var l = 0; l < hrefs.length; l++) {
+ // try {} catch{} block added by erikvold VKI
+ try{
+ //protocol, host, hostname, port, pathname, search, hash
+ if (hrefs[l].protocol == "mailto:") {
+ startListening(hrefs[l],"click",trackMailto);
+ } else if (hrefs[l].hostname == location.host) {
+ var path = hrefs[l].pathname + hrefs[l].search;
+ var isDoc = path.match(/\.(?:doc|eps|jpg|png|svg|xls|ppt|pdf|xls|zip|txt|vsd|vxd|js|css|rar|exe|wma|mov|avi|wmv|mp3|nex)($|\&|\?)/);
+ if (isDoc) {
+ startListening(hrefs[l],"click",trackExternalLinks);
+ }
+ } else if (!hrefs[l].href.match(/^javascript:/)) {
+ startListening(hrefs[l],"click",trackExternalLinks);
+ }
+ }
+ catch(e){
+ continue;
+ }
+ }
+}
+
+function startListening (obj,evnt,func) {
+ if (obj.addEventListener) {
+ obj.addEventListener(evnt,func,false);
+ } else if (obj.attachEvent) {
+ obj.attachEvent("on" + evnt,func);
+ }
+}
+
+function trackMailto (evnt) {
+ var href = (evnt.srcElement) ? evnt.srcElement.href : this.href;
+ var mailto = "/mailto/" + href.substring(7);
+ if (typeof(pageTracker) == "object") pageTracker._trackPageview(mailto);
+}
+
+function trackExternalLinks (evnt) {
+ var e = (evnt.srcElement) ? evnt.srcElement : this;
+ while (e.tagName != "A") {
+ e = e.parentNode;
+ }
+ var lnk = (e.pathname.charAt(0) == "/") ? e.pathname : "/" + e.pathname;
+ if (e.search && e.pathname.indexOf(e.search) == -1) lnk += e.search;
+ if (e.hostname != location.host) lnk = "/external/" + e.hostname + lnk;
+ if (typeof(pageTracker) == "object") pageTracker._trackPageview(lnk);
+}
\ No newline at end of file
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2011-05-17 19:20:07
|
Revision: 869
http://treebase.svn.sourceforge.net/treebase/?rev=869&view=rev
Author: rvos
Date: 2011-05-17 19:19:58 +0000 (Tue, 17 May 2011)
Log Message:
-----------
Using the uncompressed version for debugging purposes.
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/scripts/jsphylosvg-min.js
Modified: trunk/treebase-web/src/main/webapp/scripts/jsphylosvg-min.js
===================================================================
--- trunk/treebase-web/src/main/webapp/scripts/jsphylosvg-min.js 2011-05-16 16:38:51 UTC (rev 868)
+++ trunk/treebase-web/src/main/webapp/scripts/jsphylosvg-min.js 2011-05-17 19:19:58 UTC (rev 869)
@@ -1,73 +1,2491 @@
-Smits={};
-Smits.Common={nodeIdIncrement:0,activeNode:0,roundFloat:function(a,c){for(var b=0,f=1;b<c;)f*=10,b++;return Math.round(a*f)/f},apply:function(a,c){if(a&&typeof c=="object")for(var b in c)a[b]=c[b];return a},addEventHandler:function(a,c,b,f){try{a.addEventListener(c,function(a){return function(c){f.e=c;a(f)}}(b,f),!1)}catch(l){}},isInteger:function(a){return!isNaN(parseInt(a))},isXMLSerializerAvailable:function(){return typeof XMLSerializer=="function"?!0:!1},createSvgEl:function(a,c){a=document.createElementNS("http://www.w3.org/2000/svg",a);
-if(c)for(var b in c)c.hasOwnProperty(b)&&a.setAttribute(b,String(c[b]));return a},createGradientEl:function(a,c,b){if(c.type!="radialGradient")return!1;a=Smits.Common.createSvgEl("radialGradient",{id:a,gradientUnits:"userSpaceOnUse",cx:b[0],cy:b[1],r:b[2],fx:b[0],fy:b[1]});if(c.stop){c=c.stop;for(b=0;b<c.length;b++){var f=c[b];f["@attributes"]?a.appendChild(Smits.Common.createSvgEl("stop",f["@attributes"])):(f._attributes&&delete f._attributes,f._children&&delete f._children,f.__proto__&&delete f.__proto__,
-a.appendChild(Smits.Common.createSvgEl("stop",f)))}}return a},setCssStyle:function(a,c){var b=document.styleSheets[0];b.addRule?b.addRule(a,c):b.insertRule&&b.insertRule(a+" { "+c+" }",b.cssRules.length)}};
-Smits.PhyloCanvas=function(){var a,c,b,f;return function(l,m,q,g,n){this.getNewickObject=function(){};this.clear=function(){};this.scale=function(d){b.svg.scale(d)};this.getSvg=function(){return b};this.getPhylogram=function(){return a};this.getSvgSource=function(){return Raphael.svg&&Smits.Common.isXMLSerializerAvailable()?(new XMLSerializer).serializeToString(b.svg.canvas):!1};if(typeof l==="object")if(l.xml){var d=l.fileSource?l.xml:XMLObjectifier.textToXML(l.xml),d=XMLObjectifier.xmlToJSON(d);
-f=new Smits.PhyloCanvas.PhyloxmlParse(d)}else l.phyloxml?(d=l.fileSource?l.phyloxml:XMLObjectifier.textToXML(l.phyloxml),d=XMLObjectifier.xmlToJSON(d),f=new Smits.PhyloCanvas.PhyloxmlParse(d)):l.nexml?(d=l.fileSource?l.nexml:XMLObjectifier.textToXML(l.nexml),d=XMLObjectifier.xmlToJSON(d),f=new Smits.PhyloCanvas.NexmlParse(d,l)):l.json?f=new Smits.PhyloCanvas.PhyloxmlParse(l.json):l.newick?f=new Smits.PhyloCanvas.NewickParse(l.newick):l.nexmlJson?f=new Smits.PhyloCanvas.NexmlJsonParse(l):alert("Please set the format of input data");
-else f=new Smits.PhyloCanvas.NewickParse(l);c=m;b=new Smits.PhyloCanvas.Render.SVG(c,q,g);a=n=="circular"?new Smits.PhyloCanvas.Render.CircularPhylogram(b,f):new Smits.PhyloCanvas.Render.Phylogram(b,f)}}();Smits.PhyloCanvas.prototype={};Smits.PhyloCanvas.Node=function(){return function(a,c){this.id=Smits.Common.nodeIdIncrement+=1;this.newickLen=this.len=this.level=0;this.type=this.name="";this.chart={};this.img=[];a&&Smits.Common.apply(this,a);this.children=[];c&&c.children.push(this)}}();
-Smits.PhyloCanvas.Node.prototype={getCountAllChildren:function(){var a=0,c;for(c in this.children)if(Smits.Common.isInteger(c)){var b=this.children[c];b.children&&b.children.length>0?a+=b.getCountAllChildren():a++}return a},getCountImmediateChildren:function(){var a=0,c;for(c in this.children)a+=this.children[c].length;return a},getMidbranchPosition:function(){for(var a=[0,0],c=0;c<this.children.length;c++){var b=this.children[c];b.children&&b.children.length>0?c==0?(a[0]=b.getMidbranchPosition(),
-a[1]+=b.getCountAllChildren()):a[1]+=c==this.children.length-1?b.getMidbranchPosition():b.getCountAllChildren():(c==0&&(a[0]=1),a[1]+=1)}return a[1]>=a[0]?(a[1]-a[0])/2+a[0]:a[0]}};
-Smits.PhyloCanvas.NewickParse=function(){var a,c,b,f=0,l=0,m,q=function(a){for(var e=new Smits.PhyloCanvas.Node;c!==")"&&c!==",";)if(c===":"){if(d(),e.len=Smits.Common.roundFloat(n(),4),e.len==0)e.len=1.0E-4}else if(c==="'"||c==='"'){e.type="label";for(var g=e,k=c,b="";c!==k;)b+=c,d();g.name=b}else e.type="label",e.name=n();e.level=a.level+1;return e},g=function(a){var e=new Smits.PhyloCanvas.Node;if(a)e.level=a.level+1;for(;c!==")";)d(),c==="("?e.children.push(g(e)):e.children.push(q(e));d();if(c!==
-":"&&c!==")"&&c!==","&&c!==";")e.type="label",e.name=n();if(c===":"){d();e.len=Smits.Common.roundFloat(n(),4);if(e.len==0)e.len=1.0E-4;e.type="stem"}return e},n=function(){for(var a="";c!==":"&&c!==")"&&c!==","&&c!==";";)a+=c,d();return a},d=function(){c=a.charAt(b);b+=1;return c},k=function(d){if(d.children&&d.children.length)for(var a=0;a<d.children.length;a++){var c=d.children[a];if(c.len===0)c.len=1;c.newickLen=Smits.Common.roundFloat(c.len+d.newickLen,4);if(c.level>f)f=c.level;if(c.newickLen>
-l)l=c.newickLen;c.children.length>0&&k(c,d)}return d};return function(c){this.getRoot=function(){return m};this.getLevels=function(){return f};this.getNewickLen=function(){return l};this.getValidate=function(){};a=c;b=0;d();m=g();m=k(m)}}();Smits.PhyloCanvas.NewickParse.prototype={};
-Smits.PhyloCanvas.PhyloxmlParse=function(){var a=0,c=0,b,f,l=function(a,c){var d=new Smits.PhyloCanvas.Node;if(c)d.level=c.level+1;if(a.clade&&a.clade.length)for(var k=0;k<a.clade.length;k++)d.children.push(l(a.clade[k],d));if(a.branch_length){if(typeof a.branch_length==="object")a.branch_length=a.branch_length[0].Text;d.len=Smits.Common.roundFloat(a.branch_length,4);if(d.len==0)d.len=1.0E-4}if(a.name){d.type="label";d.name=a.name[0].Text;if(a.name[0]&&a.name[0].style)d.style=a.name[0].style;if(a.name[0]&&
-a.name[0].bgStyle)d.bgStyle=a.name[0].bgStyle}else if(a.confidence)d.name=a.confidence[0].Text;if(a.sequence&&a.sequence[0]&&a.sequence[0].name&&a.sequence[0].name[0]&&a.sequence[0].name[0].Text)d.sequenceName=a.sequence[0].name[0].Text;if(a.taxonomy&&a.taxonomy[0]){if(a.taxonomy[0].scientific_name&&a.taxonomy[0].scientific_name[0]&&a.taxonomy[0].scientific_name[0].Text)d.taxonomyScientificName=a.taxonomy[0].scientific_name[0].Text;if(a.taxonomy[0].common_name&&a.taxonomy[0].common_name[0]&&a.taxonomy[0].common_name[0].Text)d.taxonomyCommonName=
-a.taxonomy[0].common_name[0].Text}if(a.sequence&&a.sequence[0]&&a.sequence[0].accession&&a.sequence[0].accession[0]&&a.sequence[0].accession[0].Text)d.sequenceAccession=a.sequence[0].accession[0].Text;if(a.point)d.LatLong=[a.point[0].lat[0].Text,a.point[0]["long"][0].Text];if(!d.name){if(d.sequenceName)d.name=d.sequenceName;else if(d.taxonomyScientificName)d.name=d.taxonomyScientificName;else if(d.taxonomyCommonName)d.name=d.taxonomyCommonName;else if(d.sequenceAccession)d.name=d.sequenceAccession;
-if(d.name)d.type="label"}if(a.annotation){if(a.annotation[0]&&a.annotation[0].desc&&a.annotation[0].desc[0]&&a.annotation[0].desc[0].Text)d.description=a.annotation[0].desc[0].Text;if(a.annotation[0]&&a.annotation[0].uri&&a.annotation[0].uri[0]&&a.annotation[0].uri[0].Text)d.uri=a.annotation[0].uri[0].Text;if(a.annotation[0]&&a.annotation[0].img)for(k in a.annotation[0].img)if(Smits.Common.isInteger(k))d.img[k]=a.annotation[0].img[k].Text}if(a.chart&&a.chart[0])for(k in a.chart[0])if(k!="Text"&&k!=
-"_children")d.chart[k]=a.chart[0][k][0].Text;d&&d.level>1&&(d.len||(f="Error. Please include Branch Lengths - we only draw rooted phylogenetic trees."));return d},m=function(b){if(b.children&&b.children.length)for(var f=0;f<b.children.length;f++){var d=b.children[f];d.newickLen=Math.round((d.len+b.newickLen)*1E4)/1E4;if(d.level>a)a=d.level;if(d.newickLen>c)c=d.newickLen;d.children.length>0&&m(d,b)}return b},q=function(a,c){for(var d in a)d!="_children"&&d!="Text"&&(d=="rectangular"||d=="circular"?
-q(a[d][0],d):(Smits.PhyloCanvas.Render.Parameters[d]||(Smits.PhyloCanvas.Render.Parameters[d]={}),Smits.PhyloCanvas.Render.Parameters.set(d,a[d][0].Text,c)))};return function(g){this.getRoot=function(){return b};this.getLevels=function(){return a};this.getNewickLen=function(){return c};this.getValidate=function(){return f};g.phylogeny&&g.phylogeny[0]&&g.phylogeny[0].clade&&(b=l(g.phylogeny[0].clade[0]));if(g.phylogeny&&g.phylogeny[0]&&g.phylogeny[0].render&&g.phylogeny[0].render[0]){if((g=g.phylogeny[0].render[0])&&
-g.styles){var n=g.styles[0],d;for(d in n)if(d!="_children"&&d!="Text")if(n[d][0].type&&n[d][0].type=="radialGradient"&&Raphael.svg)n[d][0].name=d,Smits.PhyloCanvas.Render.Style[d]=n[d][0],Smits.PhyloCanvas.Render.Style.jsphylosvgGradientList||(Smits.PhyloCanvas.Render.Style.jsphylosvgGradientList=[]),Smits.PhyloCanvas.Render.Style.jsphylosvgGradientList.push(d);else for(var k in Smits.PhyloCanvas.Render.Style[d]||(Smits.PhyloCanvas.Render.Style[d]={}),n[d][0])k!="_attributes"&&k!="_children"&&k!=
-"type"&&(Smits.PhyloCanvas.Render.Style[d][k.replace("_","-")]=n[d][0][k])}g&&g.parameters&&q(g.parameters[0]);if(g&&g.charts)for(d in g=g.charts[0],g)if(d!="_children"&&d!="Text")for(k in g[d])if(g[d][k].type=="binary")g[d][k].chart=d,Smits.PhyloCanvas.Render.Parameters.binaryCharts.push(g[d][k]);else if(g[d][k].type=="integratedBinary")g[d][k].chart=d,Smits.PhyloCanvas.Render.Parameters.integratedBinaryCharts.push(g[d][k]);else if(g[d][k].type=="bar")g[d][k].chart=d,Smits.PhyloCanvas.Render.Parameters.barCharts.push(g[d][k])}b=
-m(b)}}();Smits.PhyloCanvas.PhyloxmlParse.prototype={};
-Smits.PhyloCanvas.NexmlParse=function(){var a=0,c=0,b,f,l,m,q=function(a,d,c){var j=new Smits.PhyloCanvas.Node;if(c)j.level=c.level+1;for(c=0;c<l.length;c++)if(l[c].source==a.id)for(var e=0;e<m.length;e++)l[c].target==m[e].id&&j.children.push(q(m[e],l[c].length,j));if(d&&(j.len=Smits.Common.roundFloat(d,4),j.len==0))j.len=1.0E-4;if(a.label&&(j.type="label",j.name=a.label,a.style))j.style=a.style;j&&j.level>1&&(j.len||(f="Error. Please include Branch Lengths - we only draw rooted phylogenetic trees."));return j},
-g=function(b){if(b.children&&b.children.length)for(var d=0;d<b.children.length;d++){var k=b.children[d];k.newickLen=Math.round((k.len+b.newickLen)*1E4)/1E4;if(k.level>a)a=k.level;if(k.newickLen>c)c=k.newickLen;k.children.length>0&&g(k,b)}return b};return function(n,d){this.getRoot=function(){return b};this.getLevels=function(){return a};this.getNewickLen=function(){return c};this.getValidate=function(){return f};d.tree&&n.trees[0]&&n.trees[0].tree[d.tree-1]?(l=n.trees[0].tree[d.tree-1].edge,m=n.trees[0].tree[d.tree-
-1].node):(l=n.trees[0].tree[0].edge,m=n.trees[0].tree[0].node);for(i=0;i<m.length;i++)m[i].root&&m[i].root=="true"&&(b=m[i]);b?(b=q(b),b=g(b)):f="Error. Currently, only rooted NeXML trees are supported."}}();Smits.PhyloCanvas.NexmlParse.prototype={};
-Smits.PhyloCanvas.NexmlJsonParse=function(){var a=0,c=0,b,f,l=[],m=[],q=function(a,c,j){var e=new Smits.PhyloCanvas.Node;if(j)e.level=j.level+1;for(j=0;j<l.length;j++)if(l[j].source==a.id)for(var b=0;b<m.length;b++)l[j].target==m[b].id&&e.children.push(q(m[b],l[j].length,e));if(c&&(e.len=Smits.Common.roundFloat(c,4),e.len==0))e.len=1.0E-4;if(a.label){e.type="label";e.name=a.label;if(a.accession)e.accession=a.accession;if(a.style)e.style=a.style;if(a.bgStyle)e.bgStyle=a.bgStyle}if(a.chart)e.chart=
-a.chart;e&&e.level>1&&(e.len||(f="Error. Please include Branch Lengths - we only draw rooted phylogenetic trees."));return e},g=function(d){if(d.children&&d.children.length)for(var b=0;b<d.children.length;b++){var j=d.children[b];j.newickLen=Math.round((j.len+d.newickLen)*1E4)/1E4;if(j.level>a)a=j.level;if(j.newickLen>c)c=j.newickLen;j.children.length>0&&g(j,d)}return d},n=function(a,c){for(var b in a)b!="_children"&&b!="Text"&&(b=="rectangular"||b=="circular"?n(a[b],b):(Smits.PhyloCanvas.Render.Parameters[b]||
-(Smits.PhyloCanvas.Render.Parameters[b]={}),Smits.PhyloCanvas.Render.Parameters.set(b,a[b],c)))};return function(d){this.getRoot=function(){return b};this.getLevels=function(){return a};this.getNewickLen=function(){return c};this.getValidate=function(){return f};var k=d.nexmlJson.nexml,j=k.render;if(j&&j.styles){var e=j.styles,h;for(h in e)if(h!="_children"&&h!="Text")if(e[h]["@attributes"].type&&e[h]["@attributes"].type=="radialGradient"&&Raphael.svg)e[h].name=h,e[h].type=e[h]["@attributes"].type,
-Smits.PhyloCanvas.Render.Style[h]=e[h],Smits.PhyloCanvas.Render.Style.jsphylosvgGradientList||(Smits.PhyloCanvas.Render.Style.jsphylosvgGradientList=[]),Smits.PhyloCanvas.Render.Style.jsphylosvgGradientList.push(h);else for(var o in Smits.PhyloCanvas.Render.Style[h]||(Smits.PhyloCanvas.Render.Style[h]={}),e[h]["@attributes"])o!="_attributes"&&o!="_children"&&o!="type"&&(Smits.PhyloCanvas.Render.Style[h][o.replace("_","-")]=e[h]["@attributes"][o])}j&&j.parameters&&n(j.parameters);if(j&&j.charts)for(h in j=
-j.charts,j)j[h]["@attributes"].chart=h,j[h]["@attributes"].type=="binary"?Smits.PhyloCanvas.Render.Parameters.binaryCharts.push(j[h]["@attributes"]):j[h]["@attributes"].type=="integratedBinary"?Smits.PhyloCanvas.Render.Parameters.integratedBinaryCharts.push(j[h]["@attributes"]):j[h]["@attributes"].type=="bar"&&Smits.PhyloCanvas.Render.Parameters.barCharts.push(j[h]["@attributes"]);if(d.tree&&k.trees[0]&&k.trees[0].tree[d.tree-1])l=k.trees[0].tree[d.tree-1].edge,m=k.trees[0].tree[d.tree-1].node;else{for(h=
-0;h<k.trees.tree.edge.length;h++)l.push(k.trees.tree.edge[h]["@attributes"]);for(h=0;h<k.trees.tree.node.length;h++){d=k.trees.tree.node[h]["@attributes"];if(d.label)d.chart=k.trees.tree.node[h].chart;m.push(d)}}for(h=0;h<m.length;h++)m[h].root&&m[h].root=="true"&&(b=m[h]);b?(b=q(b),b=g(b)):f="Error. Currently, only rooted NeXML trees are supported."}}();Smits.PhyloCanvas.NexmlParse.prototype={};Smits.PhyloCanvas.Render={};
-Smits.PhyloCanvas.Render.Style={line:{stroke:"rgb(0,0,0)","stroke-width":1},text:{"font-family":"Verdana","font-size":12,"text-anchor":"start"},path:{stroke:"rgb(0,0,0)","stroke-width":1},connectedDash:{stroke:"rgb(200,200,200)","stroke-dasharray":". "},textSecantBg:{fill:"#EEE",stroke:"#DDD"},highlightedEdgeCircle:{fill:"red"},barChart:{fill:"#003300",stroke:"#DDD"},getStyle:function(a,c){return this[a]?this[a]:this[c]}};
-Smits.PhyloCanvas.Render.Parameters={jsOverride:0,Rectangular:{bufferX:200,bufferY:40,bufferInnerLabels:10,bufferOuterLabels:5,minHeightBetweenLeaves:10,alignPadding:0,alignRight:!1,showScaleBar:!1},Circular:{bufferRadius:0.33,bufferAngle:20,initStartAngle:160,innerCircleRadius:0,minHeightBetweenLeaves:5,bufferInnerLabels:2,bufferOuterLabels:5},binaryCharts:[],integratedBinaryCharts:[],barCharts:[],binaryChartBufferInner:5,binaryChartBufferSiblings:0.01,binaryChartThickness:15,binaryChartDisjointed:!1,
-barChartBufferInner:3,barChartHeight:50,barChartWidth:0.5,mouseRollOver:function(a){if(a.node.edgeCircleHighlight)a.node.edgeCircleHighlight.show();else{var c=a.svg.draw(new Smits.PhyloCanvas.Render.Circle(a.x,a.y,5,{attr:Smits.PhyloCanvas.Render.Style.highlightedEdgeCircle}));a.node.edgeCircleHighlight=c[0]}a.textEl.attr({fill:"red"})},mouseRollOut:function(a){a.node.edgeCircleHighlight.hide();a.textEl.attr({fill:"#000"})},set:function(a,c,b){this.jsOverride||(b?b=="circular"?this.Circular[a]=parseFloat(c):
-b=="rectangular"&&(this.Rectangular[a]=parseFloat(c)):this[a]=parseFloat(c))}};Smits.PhyloCanvas.Render.Line=function(){return function(a,c,b,f,l){this.type="line";this.attr=Smits.PhyloCanvas.Render.Style.line;this.x1=a;this.x2=c;this.y1=b;this.y2=f;if(l&&(Smits.Common.apply(this,l),l.attr))this.attr=l.attr}}();
-Smits.PhyloCanvas.Render.Text=function(){return function(a,c,b,f){this.type="text";this.attr=Smits.PhyloCanvas.Render.Style.text;this.x=a;this.y=c;this.text=b;if(f&&(Smits.Common.apply(this,f),f.attr))this.attr=f.attr}}();Smits.PhyloCanvas.Render.Path=function(){return function(a,c){this.type="path";this.attr=Smits.PhyloCanvas.Render.Style.path;this.path=a;if(c&&(Smits.Common.apply(this,c),c.attr))this.attr=c.attr}}();
-Smits.PhyloCanvas.Render.Circle=function(){return function(a,c,b,f){this.type="circle";this.x=a;this.y=c;this.radius=b;if(f&&(Smits.Common.apply(this,f),f.attr))this.attr=f.attr}}();Smits.PhyloCanvas.Render.SVG=function(){return function(a,c,b){this.canvasSize=[c,b];this.svg=Raphael(a,this.canvasSize[0],this.canvasSize[1])}}();
-Smits.PhyloCanvas.Render.SVG.prototype={render:function(){for(var a=this.phylogramObject.getDrawInstructs(),c=0;c<a.length;c++)if(a[c].type=="line")this.svg.path(["M",a[c].x1,a[c].y1,"L",a[c].x2,a[c].y2]).attr(Smits.PhyloCanvas.Render.Style.line);else if(a[c].type=="path")this.svg.path(a[c].path).attr(a[c].attr);else if(a[c].type=="circle")this.svg.circle(a[c].x,a[c].y,a[c].radius).attr({stroke:"red"});else{var b=this.svg.text(a[c].x,a[c].y,a[c].text).attr(Smits.PhyloCanvas.Render.Style.text);a[c].attr&&
-b.attr(a[c].attr);a[c].rotate&&b.rotate(a[c].rotate);b.getBBox()}},draw:function(a){var c,b;a.type=="line"?c=this.svg.path(["M",a.x1,a.y1,"L",a.x2,a.y2]).attr(Smits.PhyloCanvas.Render.Style.line):a.type=="path"?c=this.svg.path(a.path).attr(a.attr):a.type=="circle"?c=this.svg.circle(a.x,a.y,a.radius).attr({stroke:"red"}):a.type=="text"&&(c=this.svg.text(a.x,a.y,a.text).attr(Smits.PhyloCanvas.Render.Style.text),a.attr&&c.attr(a.attr),a.rotate&&c.rotate(a.rotate),a=c.getBBox(),b=Math.sqrt(a.height*a.height+
-a.width*a.width));return[c,b]}};
-Smits.PhyloCanvas.Render.Phylogram=function(){var a,c=Smits.PhyloCanvas.Render.Parameters.Rectangular,b,f,l,m,q,g,n=!0,d=0,k=0,j,e,h,o,p=[],r=function(b,e){b.len&&(n?n=!1:b.children.length==0&&(d=Smits.Common.roundFloat(d+m,4)));if(b.children.length>0){var j=[],h,f,o,g;b.len&&(h=e,f=e=Smits.Common.roundFloat(e+l*b.len,4),g=o=d+b.getMidbranchPosition()*m,a.draw(new Smits.PhyloCanvas.Render.Line(h,f,o,g)));if(b.name){h={};h=Smits.PhyloCanvas.Render.Style.getStyle("bootstrap","text");if(b.uri)h.href=
-b.uri;if(b.description)h.title=b.description;if(b.level==0){f=2;var u=d+b.getMidbranchPosition()*m}else u=g;a.draw(new Smits.PhyloCanvas.Render.Text(f+5,u,b.name,{attr:h}))}if(b.children&&b.children.length)for(f=0;f<b.children.length;f++)j.push(r(b.children[f],e));h=[];for(f=0;f<j.length;f++)j[f][0]&&h.push(j[f][0]),j[f][1]&&h.push(j[f][1]);j=Math.min.apply(null,h);h=Math.max.apply(null,h);a.draw(new Smits.PhyloCanvas.Render.Path(["M",e+1.0E-4,j,"L",e,j,"L",e,h,"L",e+1.0E-4,h],{attr:Smits.PhyloCanvas.Render.Style.line}))}else if(h=
-e,f=Smits.Common.roundFloat(e+l*b.len,2),g=o=d,b.y=d,p.push(b),a.draw(new Smits.PhyloCanvas.Render.Line(h,f,o,g)),c.alignRight&&a.draw(new Smits.PhyloCanvas.Render.Path(["M",f,o,"L",c.alignPadding+q,g],{attr:Smits.PhyloCanvas.Render.Style.connectedDash})),b.name){h={};b.style&&(h=Smits.PhyloCanvas.Render.Style.getStyle(b.style,"text"));h["text-anchor"]="start";if(b.uri)h.href=b.uri;if(b.description)h.title=b.description;j=a.draw(new Smits.PhyloCanvas.Render.Text(c.alignRight?q+c.bufferInnerLabels+
-c.alignPadding:f+c.bufferInnerLabels,g,b.name,{attr:h}));b.style&&console.log([b,h]);k=Math.max(j[1],k);Smits.PhyloCanvas.Render.Parameters.mouseRollOver&&Smits.Common.addEventHandler(j[0].node,"mouseover",Smits.PhyloCanvas.Render.Parameters.mouseRollOver,{svg:a,node:b,x:f,y:g,textEl:j[0]});Smits.PhyloCanvas.Render.Parameters.mouseRollOut&&Smits.Common.addEventHandler(j[0].node,"mouseout",Smits.PhyloCanvas.Render.Parameters.mouseRollOut,{svg:a,node:b,x:f,y:g,textEl:j[0]});Smits.PhyloCanvas.Render.Parameters.onClickAction&&
-Smits.Common.addEventHandler(j[0].node,"click",Smits.PhyloCanvas.Render.Parameters.onClickAction,{svg:a,node:b,x:f,y:g,textEl:j[0]})}return[o,g]},u=function(d,c,b){for(var e=(b&&b.bufferInner?b.bufferInner:0)|Smits.PhyloCanvas.Render.Parameters.binaryChartBufferInner,j=(b&&b.bufferSiblings?b.bufferSiblings*m:0)|(Smits.PhyloCanvas.Render.Parameters.binaryChartBufferSiblings<1?m*Smits.PhyloCanvas.Render.Parameters.binaryChartBufferSiblings:Smits.PhyloCanvas.Render.Parameters.binaryChartBufferSiblings),
-b=(b&&b.thickness?b.thickness:0)|Smits.PhyloCanvas.Render.Parameters.binaryChartThickness,h=0;h<p.length;h++){var k=p[h];a.draw(new Smits.PhyloCanvas.Render.Path(["M",d+e,k.y-m/2+j/2,"L",d+e+b,k.y-m/2+j/2,"L",d+e+b,k.y+m/2-j/2,"L",d+e,k.y+m/2-j/2,"Z"],{attr:Smits.PhyloCanvas.Render.Style.getStyle(k.chart[c],"textSecantBg")}))}return d+e+b},A=function(d,c,b){for(var e=[],j=b&&b.bufferInner?b.bufferInner:0|Smits.PhyloCanvas.Render.Parameters.barChartBufferInner,h=b&&b.height?b.height:0|Smits.PhyloCanvas.Render.Parameters.barChartHeight,
-b=b&&b.width?b.width<1?m*b.width:b.width:0|(Smits.PhyloCanvas.Render.Parameters.barChartWidth<1?m*Smits.PhyloCanvas.Render.Parameters.barChartWidth:Smits.PhyloCanvas.Render.Parameters.barChartWidth),k=0,f=0;f<p.length;f++)e.push(p[f].chart[c]);e=Math.max.apply(null,e);k=Smits.Common.roundFloat(h/e,4);for(f=0;f<p.length;f++)e=p[f],a.draw(new Smits.PhyloCanvas.Render.Path(["M",d+j,e.y-b/2,"L",d+j+k*e.chart[c],e.y-b/2,"L",d+j+k*e.chart[c],e.y+b/2,"L",d+j,e.y+b/2,"Z"],{attr:Smits.PhyloCanvas.Render.Style.getStyle(e.chart[c],
-"barChart")}));return d+j+h};return function(p,n){d=0;this.getCanvasSize=function(){return[b,f]};this.getRoot=function(){return n.getRoot()};n.getValidate()&&a.draw(0,0,n.getValidate());a=p;var t=n.getRoot(),C=n.getNewickLen();b=a.canvasSize[0];f=a.canvasSize[1];h=c.bufferX;o=c.bufferY;g=c.minHeightBetweenLeaves;l=Math.round((b-h)/C);m=Math.round((f-o)/(c.showScaleBar?t.getCountAllChildren()+1:t.getCountAllChildren()));m<g&&(m=g);q=Math.round(b-h);if(Smits.PhyloCanvas.Render.Parameters.binaryCharts.length||
-Smits.PhyloCanvas.Render.Parameters.barCharts.length)c.alignRight=!0;r(t,0);c.showScaleBar&&(y=d+m,e=c.showScaleBar*l,a.draw(new Smits.PhyloCanvas.Render.Line(0,e,y,y)),a.draw(new Smits.PhyloCanvas.Render.Text((0+e)/2,y-8,c.showScaleBar)));j=q+k+c.bufferInnerLabels;if(Smits.PhyloCanvas.Render.Parameters.binaryCharts.length){var t=Smits.PhyloCanvas.Render.Parameters.binaryCharts,s;for(s in t)j=u(j,t[s].chart,t[s])}if(Smits.PhyloCanvas.Render.Parameters.barCharts.length)for(s in t=Smits.PhyloCanvas.Render.Parameters.barCharts,
-t)A(j,t[s].chart,t[s])}}();Smits.PhyloCanvas.Render.Phylogram.prototype={};
-Smits.PhyloCanvas.Render.CircularPhylogram=function(){function a(a,d){d+=E;return[Smits.Common.roundFloat(t+a*Math.sin(d*G),4),Smits.Common.roundFloat(C+a*Math.cos(d*G),4)]}function c(a){a=l(90-a-E);if(a>90&&a<270){a+=180;var d="end"}else d="start";return[a,d]}function b(d,b,c,e){var j=a(d,b),h=a(d,c),k=[],f=0,b=Math.abs(l(c-b))>180?1:-1;e&&e.invertSecant&&(b*=-1,f=1);(!e||!e.noMove)&&k.push("M");k.push(j[0],j[1],"A",d,d,0,b<1?0:1,f,h[0],h[1]);return k}function f(d,b,c,e){var j=[],b=a(b,d),d=a(c,
-d);(!e||!e.noMove)&&j.push("M");j.push(b[0],b[1],"L",d[0],d[1]);return j}function l(a){for(;a>360||a<0;)a>360?a-=360:a<0&&(a+=360);return a}function m(a,d,c,e){!d&&a.length>1&&(e=a[3],c=a[2],d=a[1],a=a[0]);return g("M",b(a,c,e,{noMove:1,invertSecant:0}),"L",b(d,e,c,{noMove:1,invertSecant:1}),"Z")}function q(d,h){d.len&&(F?(B=D||1,F=!1):d.children.length==0&&(B=Smits.Common.roundFloat(B+u,4)));if(d.children.length>0){var k=[],p,l,o;p=h;l=h+=Smits.Common.roundFloat(r*d.len,4);if(d.children&&d.children.length)for(var m=
-0;m<d.children.length;m++){var n=q(d.children[m],h);n>0&&k.push(n)}m=Smits.Common.roundFloat(Math.min.apply(null,k),4);k=Smits.Common.roundFloat(Math.max.apply(null,k),4);j.draw(new Smits.PhyloCanvas.Render.Path(g("M",a(h+0.01,m),"L",b(h,m,k,{noMove:!0}),"L",a(h+0.01,k))));d.len&&(o=Smits.Common.roundFloat(m+(k-m)/2,4),j.draw(new Smits.PhyloCanvas.Render.Path(f(o,p,l))))}else if(d.y=B,w.push(d),p=h,l=Smits.Common.roundFloat(h+r*d.len),o=B,j.draw(new Smits.PhyloCanvas.Render.Path(f(o,p,l))),j.draw(new Smits.PhyloCanvas.Render.Path(f(o,
-l,s),{attr:Smits.PhyloCanvas.Render.Style.connectedDash})),d.name){p=a(s+e.bufferInnerLabels,o);m=c(o);k=m[0];m=m[1];n={};d.style&&Smits.Common.apply(n,Smits.PhyloCanvas.Render.Style.getStyle(d.style,"text"));n["text-anchor"]=m;if(d.uri)n.href=d.uri;if(d.description)n.title=d.description;k=j.draw(new Smits.PhyloCanvas.Render.Text(p[0],p[1],d.name,{attr:n,rotate:[k,p[0],p[1]]}));d.bgStyle&&v.push([d.bgStyle,o]);p=a(l,o);Smits.PhyloCanvas.Render.Parameters.mouseRollOver&&Smits.Common.addEventHandler(k[0].node,
-"mouseover",Smits.PhyloCanvas.Render.Parameters.mouseRollOver,{svg:j,node:d,x:p[0],y:p[1],textEl:k[0]});Smits.PhyloCanvas.Render.Parameters.mouseRollOut&&Smits.Common.addEventHandler(k[0].node,"mouseout",Smits.PhyloCanvas.Render.Parameters.mouseRollOut,{svg:j,node:d,x:p[0],y:p[1],textEl:k[0]});Smits.PhyloCanvas.Render.Parameters.onClickAction&&Smits.Common.addEventHandler(k[0].node,"click",Smits.PhyloCanvas.Render.Parameters.onClickAction,{svg:j,node:d,x:p[0],y:p[1],textEl:k[0]});z=Math.max(k[1],
-z)}return o}function g(a){for(var d=a,b=1;b<arguments.length;b++)d=d.concat(arguments[b]);return d}function n(){var a=[];if(v.length>0){if(Smits.PhyloCanvas.Render.Style.jsphylosvgGradientList)for(var d=0;d<Smits.PhyloCanvas.Render.Style.jsphylosvgGradientList.length;d++){var b=Smits.PhyloCanvas.Render.Style.jsphylosvgGradientList[d],b=Smits.Common.createGradientEl(b,Smits.PhyloCanvas.Render.Style[b],[t,C,s+z+e.bufferOuterLabels]);j.svg.defs.appendChild(b)}for(d=0;d<v.length;d++)d!=v.length-1&&v[d][0]==
-v[d+1][0]?v[d+1][2]=v[d][2]?v[d][2]:v[d][1]:(a=m(s,s+z+e.bufferOuterLabels,v[d][2]?v[d][2]-u/2:v[d][1]-u/2,v[d][1]+u/2),b=Smits.PhyloCanvas.Render.Style.getStyle(v[d][0],"textSecantBg"),a=j.draw(new Smits.PhyloCanvas.Render.Path(a,{attr:b.type?{}:b})),b.type&&b.type=="radialGradient"&&a[0].node.setAttribute("fill","url(#"+b.name+")"),b.type&&b.type=="radialGradient"&&a[0].node.setAttribute("stroke","none"),a[0].toBack())}a=m(s,s+z+e.bufferOuterLabels,(D||1)+u/2,360+u/2);a=j.draw(new Smits.PhyloCanvas.Render.Path(a,
-{attr:Smits.PhyloCanvas.Render.Style.textSecantBg}));a[0].toBack();return s+z+e.bufferOuterLabels}function d(d,b,e){for(var h=e&&e.bufferInner?parseFloat(e.bufferInner):Smits.PhyloCanvas.Render.Parameters.binaryChartBufferInner,k=(e&&e.bufferSiblings?e.bufferSiblings*u:0)|(Smits.PhyloCanvas.Render.Parameters.binaryChartBufferSiblings<1?u*Smits.PhyloCanvas.Render.Parameters.binaryChartBufferSiblings:Smits.PhyloCanvas.Render.Parameters.binaryChartBufferSiblings),f=e&&e.thickness?parseFloat(e.thickness):
-Smits.PhyloCanvas.Render.Parameters.binaryChartThickness,p=(e&&e.disjointed?e.disjointed:0)|Smits.PhyloCanvas.Render.Parameters.binaryChartDisjointed,e=e&&e.isInternal?e.isInternal:!1,o=!0,g,n=0;n<w.length;n++){var r=w[n];if((!w[n+1]||r.chart[b]!==w[n+1].chart[b]||p)&&r.chart[b]!="none"){var q=Smits.PhyloCanvas.Render.Style.getStyle(r.chart[b],"textSecantBg");g=e?[s-h-f,s-h,(g?g:r.y)-u/2+(o&&!p?0:k/2),r.y+u/2-(n==w.length-1&&!p?0:k/2)]:[d+h,d+h+f,(g?g:r.y)-u/2+(o&&!p?0:k/2),r.y+u/2-(n==w.length-1&&
-!p?0:k/2)];if(q.label){var o=Smits.PhyloCanvas.Render.Style.getStyle(q.labelStyle,"text"),r=a((g[0]+g[1])/2,(g[2]+g[3])/2),t=c((g[2]+g[3])/2),t=l(t[0]+(o.rotate?parseFloat(o.rotate):0)),v=l(90-(g[2]+g[3])/2-E);v>90&&v<270&&(t+=180);o["text-anchor"]||(o["text-anchor"]="middle");j.draw(new Smits.PhyloCanvas.Render.Text(r[0],r[1],q.label,{attr:o,rotate:t}))[0].toBack()}q.borderStyle&&(o=Smits.PhyloCanvas.Render.Style.getStyle(q.borderStyle,"textSecantBg"),j.draw(new Smits.PhyloCanvas.Render.Path(m([s,
-o.fullsize?g[1]:g[0],g[2],g[3]]),{attr:o}))[0].toBack());j.draw(new Smits.PhyloCanvas.Render.Path(m(g),{attr:q}))[0].toBack();g=0}else{if(!g)g=r.y;r.chart[b]=="none"&&(g=0)}o=!1}return e?d:d+h+f}function k(d,a,b){for(var c=[],e=b&&b.bufferInner?parseFloat(b.bufferInner):Smits.PhyloCanvas.Render.Parameters.barChartBufferInner,h=b&&b.height?parseFloat(b.height):Smits.PhyloCanvas.Render.Parameters.barChartHeight?Smits.PhyloCanvas.Render.Parameters.barChartHeight:0,b=b&&b.width?parseFloat(b.width)<1?
-u*parseFloat(b.width):parseFloat(b.width):0|(Smits.PhyloCanvas.Render.Parameters.barChartWidth<1?u*Smits.PhyloCanvas.Render.Parameters.barChartWidth:Smits.PhyloCanvas.Render.Parameters.barChartWidth),k=0,f=0;f<w.length;f++)c.push(w[f].chart[a]);c=Math.max.apply(null,c);k=Smits.Common.roundFloat(h/c,4);for(f=0;f<w.length;f++)c=w[f],c.chart[a]>0&&j.draw(new Smits.PhyloCanvas.Render.Path(m(d+e,d+e+k*c.chart[a],c.y-b/2,c.y+b/2),{attr:Smits.PhyloCanvas.Render.Style.getStyle(c.chart[a],"barChart")}));return d+
-e+h}var j,e=Smits.PhyloCanvas.Render.Parameters.Circular,h,o,p,r,u,A,F=!0,B=0,t,C,s,w=[],v=[],D,x,z=0,E,G=Math.PI/180;return function(a,b,c){this.getCanvasSize=function(){return[h,o]};this.getRoot=function(){return b.getRoot()};if(b.getValidate())a.draw({type:"text",x:0,y:a.canvasSize[1]/3,text:b.getValidate()});else{j=a;var a=b.getRoot(),f=b.getNewickLen();h=j.canvasSize[0];o=j.canvasSize[1];t=h/2;C=o/2;p=Math.min.apply(null,[h,o]);c=e.bufferRadius>1?e.bufferRadius:Smits.Common.roundFloat(p*e.bufferRadius,
-4);D=e.bufferAngle;A=e.innerCircleRadius;E=e.initStartAngle;s=Math.round((p-c-A)/2);r=(s-A)/f;u=Smits.Common.roundFloat((360-D)/a.getCountAllChildren(),4);q(a,A);x=s+z+e.bufferOuterLabels;if(Smits.PhyloCanvas.Render.Parameters.integratedBinaryCharts.length){var c=Smits.PhyloCanvas.Render.Parameters.integratedBinaryCharts,g;for(g in c)x=d(x-(c[g].thickness?c[g].thickness:Smits.PhyloCanvas.Render.Parameters.binaryChartThickness)-(c[g].bufferInner?c[g].bufferInner:Smits.PhyloCanvas.Render.Parameters.binaryChartBufferInner),
-c[g].chart,c[g])}x=n();if(Smits.PhyloCanvas.Render.Parameters.binaryCharts.length)for(g in c=Smits.PhyloCanvas.Render.Parameters.binaryCharts,c)x=d(x,c[g].chart,c[g]);if(Smits.PhyloCanvas.Render.Parameters.barCharts.length)for(g in c=Smits.PhyloCanvas.Render.Parameters.barCharts,c)x=k(x,c[g].chart,c[g])}}}();Smits.PhyloCanvas.Render.CircularPhylogram.prototype={};
-var XMLObjectifier=function(){var a=function(a){var b="";a&&typeof a==="string"&&(b=a);return/^((-)?([0-9]*)((\.{0,1})([0-9]+))?$)/.test(b)};return{xmlToJSON:function(c){try{if(!c)return null;var b={typeOf:"JSXBObject"},f=c.nodeType==9?c.documentElement:c;b.RootName=f.nodeName||"";if(c.nodeType==3||c.nodeType==4)return c.nodeValue;var l=function(a){return a.replace(/^\s+|\s+$/gm,"")},m=function(a,b){if(b.attributes.length>0){var c=b.attributes.length-1,e;a._attributes=[];do e=String(String(b.attributes[c].name).replace(/-/g,
-"_")),a._attributes.push(e),a[e]=l(b.attributes[c].value);while(c--)}};(function(){return{activate:function(){var a=[];a.getNodesByAttribute=function(b,c){if(a&&a.length>0){var e=[],h,f=a.length-1;try{do h=a[f],h[b]===c&&e.push(h);while(f--);e.reverse();return e}catch(g){}return null}};a.getNodeByAttribute=function(b,c){if(a&&a.length>0){var e,h=a.length-1;try{do if(e=a[h],e[b]===c)return e;while(h--)}catch(f){}return null}};a.getNodesByValue=function(b){if(a&&a.length>0){var c=[],e,h=a.length-1;
-try{do e=a[h],e.Text&&e.Text===b&&c.push(e);while(h--);return c}catch(f){}return null}};a.contains=function(b,c){if(a&&a.length>0){var e=a.length-1;try{do if(a[e][b]===c)return!0;while(e--)}catch(h){}return!1}};a.indexOf=function(b,c){var e=-1;if(a&&a.length>0){var h=a.length-1;try{do a[h][b]===c&&(e=h);while(h--)}catch(f){return-1}return e}};a.SortByAttribute=function(b,c){if(a&&a.length>0){var e=function(a,b){var d=a[b];return d=bam.validation.isNumeric(d)?parseFloat(d):d};a.sort(function(a,d){var f,
-g;f=e(a,b);g=e(d,b);f=f<g?-1:g<f?1:0;c&&(f=c.toUpperCase()==="DESC"?0-f:f);return f})}};a.SortByValue=function(b){if(a&&a.length>0){var c=function(a){a=a.Text;return a=bam.validation.isNumeric(a)?parseFloat(a):a};a.sort(function(a,d){var f,g;f=c(a);g=c(d);f=f<g?-1:g<f?1:0;b&&(f=b.toUpperCase()==="DESC"?0-f:f);return f})}};a.SortByNode=function(b,c){if(a&&a.length>0){var e=function(a,b){var d=a[b][0].Text;return d=bam.validation.isNumeric(d)?parseFloat(d):d};a.sort(function(a,d){var f,g;f=e(a,b);g=
-e(d,b);f=f<g?-1:g<f?1:0;c&&(f=c.toUpperCase()==="DESC"?0-f:f);return f})}};return a}}})();var q=function(b){b.getNodeByAttribute=function(a,b){if(this.length>0){var d,c=this.length-1;try{do if(d=this[c],d[a]==b)return d;while(c--)}catch(f){}return!1}};b.contains=function(a,b){if(this.length>0){var d=this.length-1;try{do if(this[d][a]==b)return!0;while(d--)}catch(c){}return!1}};b.indexOf=function(a,b){var d=-1;if(this.length>0){var c=this.length-1;try{do this[c][a]==b&&(d=c);while(c--)}catch(f){return-1}return d}};
-b.SortByAttribute=function(b,d){if(this.length){var c=function(b,d){var c=b[d];return c=a(c)?parseFloat(c):c};this.sort(function(a,f){var g=0,l,m;l=c(a,b);m=c(f,b);l<m?g=-1:m<l&&(g=1);d&&(g=d.toUpperCase()=="DESC"?0-g:g);return g})}};b.SortByValue=function(b){if(this.length){var d=function(b){b=b.Text;return b=a(b)?parseFloat(b):b};this.sort(function(a,c){var f=0,g,l;g=d(a);l=d(c);g<l?f=-1:l<g&&(f=1);b&&(f=b.toUpperCase()=="DESC"?0-f:f);return f})}};b.SortByNode=function(b,d){if(this.length){var c=
-function(b,d){var c=b[d][0].Text;return c=a(c)?parseFloat(c):c};this.sort(function(a,f){var g=0,l,m;l=c(a,b);m=c(f,b);l<m?g=-1:m<l&&(g=1);d&&(g=d.toUpperCase()=="DESC"?0-g:g);return g})}}},g=function(a,b){var c,e,f,n="";if(!b)return null;b.attributes.length>0&&m(a,b);a.Text="";if(b.hasChildNodes()){var p=b.childNodes.length-1,r=0;do switch(e=b.childNodes[r],e.nodeType){case 1:a._children=[];c=e.localName?e.localName:e.baseName;c=String(c).replace(/-/g,"_");n!=c&&a._children.push(c);a[c]||(a[c]=[]);
-f={};a[c].push(f);e.attributes.length>0&&m(f,e);a[c].contains||q(a[c]);n=c;e.hasChildNodes()&&g(f,e);break;case 3:a.Text+=l(e.nodeValue);break;case 4:a.Text+=e.text?l(e.text):l(e.nodeValue)}while(r++<p)}};g(b,f);f=c=null;return b}catch(n){return null}},textToXML:function(a){var b=null;try{b=document.all?new ActiveXObject("Microsoft.XMLDOM"):new DOMParser,b.async=!1}catch(f){throw Error("XML Parser could not be instantiated");}var l;try{l=document.all?b.loadXML(a)?b:!1:b.parseFromString(a,"text/xml")}catch(m){throw Error("Error parsing XML string");
-}return l}}}();
+Smits = {};Smits.Common = {
+ nodeIdIncrement : 0,
+ activeNode: 0,
+
+ /* Rounds float to a defined number of decimal places */
+ roundFloat : function(num, digits){
+ var i = 0,
+ dec = 1;
+ while(i < digits){
+ dec *= 10;
+ i++;
+ }
+ return Math.round(num*dec)/dec;
+ },
+
+ /* Copies properties from one object to another */
+ apply : function(obj, extObj){
+ if (obj && typeof extObj == 'object') {
+ for (var key in extObj) {
+ obj[key] = extObj[key];
+ }
+ }
+ return obj;
+ },
+
+ addEventHandler : function(el, eventType, fn, paramsObj){
+ try{
+ el.addEventListener(
+ eventType,
+ (function(fn, args){
+ return(
+ function(e,o) {
+ var params = paramsObj;
+ params.e = e;
+ fn(params);
+ }
+ );
+ }(fn, paramsObj)),
+ false
+ );
+ } catch (err){}
+ },
+
+ isInteger : function(s) {
+ return !isNaN(parseInt(s));
+ },
+
+ isXMLSerializerAvailable : function(){
+ if (typeof(XMLSerializer) == "function"){
+ return true;
+ } else {
+ return false;
+ }
+ },
+
+ createSvgEl : function (el, attr) {
+ el = document.createElementNS("http://www.w3.org/2000/svg", el);
+ if (attr) {
+ for (var key in attr) {
+ if (attr.hasOwnProperty(key)) {
+ el.setAttribute(key, String(attr[key]));
+ }
+ }
+ }
+ return el;
+ },
+
+ createGradientEl : function(name, obj, coords){
+ if(obj.type != "radialGradient") return false;
+
+ var radialEl = Smits.Common.createSvgEl("radialGradient", {
+ id: name,
+ gradientUnits:"userSpaceOnUse",
+ cx: coords[0],
+ cy: coords[1],
+ r: coords[2],
+ fx: coords[0],
+ fy: coords[1]
+ });
+
+ if(obj.stop){
+ var stop = obj.stop;
+ for(var i = 0; i < stop.length; i++){
+ var stopObj = stop[i];
+ if(stopObj['@attributes']){
+ radialEl.appendChild(Smits.Common.createSvgEl("stop", stopObj['@attributes']));
+ } else {
+ if(stopObj['_attributes']) delete stopObj['_attributes'];
+ if(stopObj['_children']) delete stopObj['_children'];
+ if(stopObj['__proto__']) delete stopObj['__proto__'];
+ radialEl.appendChild(Smits.Common.createSvgEl("stop", stopObj));
+ }
+ }
+ }
+
+ return radialEl;
+ },
+
+ setCssStyle : function(selector, rule) {
+ var stylesheet = document.styleSheets[0];
+ if( stylesheet.addRule ){
+ stylesheet.addRule(selector, rule);
+ } else if( stylesheet.insertRule ){
+ stylesheet.insertRule(selector + ' { ' + rule + ' }', stylesheet.cssRules.length);
+ }
+ }
+
+};Smits.PhyloCanvas = function(){
+ var phylogram,
+ divId,
+ newickObject,
+ svg,
+ dataObject;
+
+ return function(inputFormat, sDivId, canvasWidth, canvasHeight, type){
+ /* Privileged Methods */
+ this.getNewickObject = function(){
+ return newickObject;
+ };
+ this.clear = function(){
+
+ };
+ this.scale = function(multiplier){
+ svg.svg.scale(multiplier);
+ };
+ this.getSvg = function(){
+ return svg;
+ };
+ this.getPhylogram = function(){
+ return phylogram;
+ };
+ this.getSvgSource = function(){
+ if(Raphael.svg && Smits.Common.isXMLSerializerAvailable()){
+ var serialize = new XMLSerializer();
+ return serialize.serializeToString(svg.svg.canvas);
+ } else {
+ return false;
+ }
+ }
+
+ /* CONSTRUCTOR */
+
+ // Process dataset -- assume newick format, else needs to provide format
+ if(typeof inputFormat === "object"){
+ if(inputFormat.xml){ // default xml format is phyloXML
+ if(!inputFormat.fileSource){
+ var xj = XMLObjectifier.textToXML(inputFormat.xml); // assume we need to clean it up
+ } else {
+ var xj = inputFormat.xml;
+ }
+ xj = XMLObjectifier.xmlToJSON(xj);
+ dataObject = new Smits.PhyloCanvas.PhyloxmlParse(xj);
+ } else if(inputFormat.phyloxml){
+ if(!inputFormat.fileSource){
+ var xj = XMLObjectifier.textToXML(inputFormat.phyloxml); // assume we need to clean it up
+ } else {
+ var xj = inputFormat.phyloxml;
+ }
+ xj = XMLObjectifier.xmlToJSON(xj);
+ dataObject = new Smits.PhyloCanvas.PhyloxmlParse(xj);
+ } else if(inputFormat.nexml){
+ if(!inputFormat.fileSource){
+ var xj = XMLObjectifier.textToXML(inputFormat.nexml); // assume we need to clean it up
+ } else {
+ var xj = inputFormat.nexml;
+ }
+ xj = XMLObjectifier.xmlToJSON(xj);
+ dataObject = new Smits.PhyloCanvas.NexmlParse(xj, inputFormat)
+ } else if(inputFormat.json){
+ dataObject = new Smits.PhyloCanvas.PhyloxmlParse(inputFormat.json);
+ } else if(inputFormat.newick){
+ dataObject = new Smits.PhyloCanvas.NewickParse(inputFormat.newick);
+ } else if(inputFormat.nexmlJson){
+ dataObject = new Smits.PhyloCanvas.NexmlJsonParse(inputFormat);
+ } else {
+ alert('Please set the format of input data');
+ }
+ } else {
+ dataObject = new Smits.PhyloCanvas.NewickParse(inputFormat);
+ }
+
+ divId = sDivId;
+ svg = new Smits.PhyloCanvas.Render.SVG( divId, canvasWidth, canvasHeight );
+
+ /* FACTORY */
+ if(type == "circular"){
+ phylogram = new Smits.PhyloCanvas.Render.CircularPhylogram(
+ svg,
+ dataObject
+ );
+ } else {
+ phylogram = new Smits.PhyloCanvas.Render.Phylogram(
+ svg,
+ dataObject
+ );
+ }
+
+ }
+
+}();
+
+Smits.PhyloCanvas.prototype = {
+};Smits.PhyloCanvas.Node = function(){
+
+ /**
+ * Node Class
+ * Allows objects to be traversed across children
+ *
+ */
+ return function(o, parentInstance){
+ // initiate object
+ this.id = Smits.Common.nodeIdIncrement += 1;
+ this.level = 0;
+ this.len = 0;
+ this.newickLen = 0;
+ this.name = '';
+ this.type = '';
+ this.chart = {};
+ this.img = [];
+
+ if(o) Smits.Common.apply(this, o);
+
+ this.children = new Array();
+
+ if(parentInstance){
+ parentInstance.children.push(this);
+ }
+ }
+}();
+
+
+Smits.PhyloCanvas.Node.prototype = {
+
+ getCountAllChildren : function(){
+ var nodeCount = 0;
+
+ for (var key in this.children) {
+ if(Smits.Common.isInteger(key)){
+ var child = this.children[key];
+ if(child.children && child.children.length > 0){
+ nodeCount += child.getCountAllChildren();
+ } else {
+ nodeCount ++;
+ }
+ }
+ }
+ return nodeCount;
+ },
+
+ getCountImmediateChildren : function(){
+ var nodeCount = 0;
+
+ for (var key in this.children) {
+ var child = this.children[key];
+ nodeCount += child.length;
+ }
+ return nodeCount;
+ },
+
+ getMidbranchPosition : function(){
+ var y = [0,0]; // bounds
+
+ for (var i = 0; i < this.children.length; i++) {
+ var child = this.children[i];
+
+ if(child.children && child.children.length > 0){
+ if(i == 0){
+ y[0] = child.getMidbranchPosition();
+ y[1] += child.getCountAllChildren();
+ } else if (i == this.children.length - 1){
+ y[1] += child.getMidbranchPosition();
+ } else {
+ y[1] += child.getCountAllChildren();
+ }
+ } else {
+ if(i == 0){
+ y[0] = 1;
+ y[1] += 1;
+ } else if (i == this.children.length - 1){
+ y[1] += 1;
+ } else {
+ y[1] += 1;
+ }
+ }
+ }
+
+ return y[1] >= y[0] ? ((y[1] - y[0]) / 2) + y[0] : y[0];
+ }
+
+};Smits.PhyloCanvas.NewickParse = function(){
+
+ var text,
+ ch,
+ pos,
+ mLevel = 0,
+ mNewickLen = 0,
+ root,
+ validate,
+
+ object = function (parentNode) {
+ var node = new Smits.PhyloCanvas.Node();
+
+ while (ch !== ')' && ch !== ',') {
+ if (ch === ':'){
+ next();
+ node.len = Smits.Common.roundFloat(string(), 4); // round to 4 decimal places
+ if(node.len == 0){
+ node.len = 0.0001;
+ }
+ } else if (ch === "'" || ch === '"'){
+ node.type = "label";
+ node.name = quotedString(ch);
+ } else {
+ node.type = "label";
+ node.name = string();
+ }
+ }
+ node.level = parentNode.level + 1;
+ return node;
+ },
+
+ objectIterate = function(parentNode){
+ var node = new Smits.PhyloCanvas.Node();
+ if(parentNode){
+ node.level = parentNode.level + 1;
+ }
+
+ while( ch !== ')' ){
+ next()
+ if( ch === '(' ) {
+ node.children.push(objectIterate(node));
+ } else {
+ node.children.push(object(node));
+ }
+ }
+
+ next();
+ if(ch !== ':' && ch !== ')' && ch !== ',' && ch !== ';'){
+ node.type = "label";
+ node.name = string();
+ }
+ if(ch === ':'){
+ next();
+ node.len = Smits.Common.roundFloat(string(), 4);
+ if(node.len == 0){
+ node.len = 0.0001;
+ }
+ node.type = "stem";
+
+ }
+ return node;
+ },
+
+ string = function(){
+ var string = '';
+
+ while (ch !== ':' && ch !== ')' && ch !== ',' && ch !== ';'){
+ string += ch;
+ next();
+ }
+ return string;
+ },
+
+ quotedString = function(quoteType){
+ var string = '';
+
+ while (ch !== quoteType){
+ string += ch;
+ next();
+ }
+ return string;
+ },
+
+ next = function() {
+ ch = text.charAt(pos);
+ pos += 1;
+ return ch;
+ },
+
+ recursiveProcessRoot = function(node, parentNode){
+
+ if(node.children && node.children.length){
+ for( var i = 0; i < node.children.length; i++ ){
+ var child = node.children[i];
+ if(child.len === 0) { // Dendogram
+ child.len = 1;
+ }
+ child.newickLen = Smits.Common.roundFloat(child.len + node.newickLen, 4);
+ if(child.level > mLevel) mLevel = child.level;
+ if(child.newickLen > mNewickLen) mNewickLen = child.newickLen;
+ if(child.children.length > 0){
+ recursiveProcessRoot(child, node);
+ }
+ }
+ }
+ return node;
+ };
+
+ return function(parseText){
+ /* Privileged Methods */
+ this.getRoot = function(){
+ return root;
+ };
+ this.getLevels = function(){
+ return mLevel;
+ };
+ this.getNewickLen = function(){
+ return mNewickLen;
+ };
+ this.getValidate = function(){
+ return validate;
+ };
+
+
+ /* CONSTRUCTOR */
+ text = parseText;
+ pos = 0;
+
+ next();
+ root = objectIterate();
+ root = recursiveProcessRoot(root);
+ }
+
+}();
+
+Smits.PhyloCanvas.NewickParse.prototype = {
+
+};Smits.PhyloCanvas.PhyloxmlParse = function(){
+
+ var mLevel = 0,
+ mNewickLen = 0,
+ root,
+ validate,
+
+ recursiveParse = function(clade, parentNode){
+ var node = new Smits.PhyloCanvas.Node();
+ if(parentNode){
+ node.level = parentNode.level + 1;
+ }
+
+ if(clade.clade && clade.clade.length){
+ for(var i = 0; i < clade.clade.length; i++){
+ var thisClade = clade.clade[i];
+ node.children.push(recursiveParse(thisClade, node));
+ }
+ }
+ if(clade.branch_length){ // Branches can be attributes or own element
+ if(typeof clade.branch_length === 'object'){
+ clade.branch_length = clade.branch_length[0].Text;
+ }
+
+ node.len = Smits.Common.roundFloat(clade.branch_length, 4); // round to 4 decimal places
+ if(node.len == 0){
+ node.len = 0.0001;
+ }
+ }
+ if(clade.name){
+ node.type = 'label';
+ node.name = clade.name[0].Text;
+ if(clade.name[0] && clade.name[0].style){
+ node.style = clade.name[0].style;
+ }
+ if(clade.name[0] && clade.name[0].bgStyle){
+ node.bgStyle = clade.name[0].bgStyle;
+ }
+ } else if(clade.confidence){
+ node.name = clade.confidence[0].Text;
+ }
+
+ /* Collect further info that might be used as a label */
+ if (clade.sequence && clade.sequence[0] && clade.sequence[0].name && clade.sequence[0].name[0] && clade.sequence[0].name[0].Text){
+ node.sequenceName = clade.sequence[0].name[0].Text;
+ }
+ if (clade.taxonomy && clade.taxonomy[0]){
+ if(clade.taxonomy[0].scientific_name && clade.taxonomy[0].scientific_name[0] && clade.taxonomy[0].scientific_name[0].Text){
+ node.taxonomyScientificName = clade.taxonomy[0].scientific_name[0].Text;
+ }
+ if (clade.taxonomy[0].common_name && clade.taxonomy[0].common_name[0] && clade.taxonomy[0].common_name[0].Text){
+ node.taxonomyCommonName = clade.taxonomy[0].common_name[0].Text;
+ }
+ }
+ if (clade.sequence && clade.sequence[0] && clade.sequence[0].accession && clade.sequence[0].accession[0] && clade.sequence[0].accession[0].Text){
+ node.sequenceAccession = clade.sequence[0].accession[0].Text;
+ }
+ if (clade.point ){
+ node.LatLong = [clade.point[0].lat[0].Text, clade.point[0]['long'][0].Text];
+ }
+
+
+ /* Prioritization of Label */
+ if(!node.name){
+ if(node.sequenceName){
+ node.name = node.sequenceName;
+ } else if (node.taxonomyScientificName){
+ node.name = node.taxonomyScientificName;
+ } else if (node.taxonomyCommonName){
+ node.name = node.taxonomyCommonName;
+ } else if (node.sequenceAccession){
+ node.name = node.sequenceAccession;
+ }
+ if(node.name){ // if name is now set, type is 'label'
+ node.type = 'label';
+ }
+ }
+
+ if(clade.annotation){
+ if(clade.annotation[0] && clade.annotation[0].desc && clade.annotation[0].desc[0] && clade.annotation[0].desc[0].Text){
+ node.description = clade.annotation[0].desc[0].Text;
+ }
+ if(clade.annotation[0] && clade.annotation[0].uri && clade.annotation[0].uri[0] && clade.annotation[0].uri[0].Text){
+ node.uri = clade.annotation[0].uri[0].Text;
+ }
+ if(clade.annotation[0] && clade.annotation[0].img){
+ for(var i in clade.annotation[0].img){
+ if(Smits.Common.isInteger(i)){
+ node.img[i] = clade.annotation[0].img[i].Text;
+ }
+ }
+ }
+ }
+ if(clade.chart){
+ if(clade.chart[0]){
+ for(var i in clade.chart[0]){
+ if(i != 'Text' && i != '_children'){
+ node.chart[i] = clade.chart[0][i][0].Text;
+ }
+ }
+ }
+
+ }
+
+ // Validation
+ if(node && node.level > 1){
+ if(!node.len){
+ validate = 'Error. Please include Branch Lengths - we only draw rooted phylogenetic trees.';
+ }
+ }
+
+ return node;
+ },
+
+ recursiveProcessRoot = function(node, parentNode){
+ if(node.children && node.children.length){
+ for( var i = 0; i < node.children.length; i++){
+ var child = node.children[i];
+ child.newickLen = Math.round( (child.len + node.newickLen) *10000)/10000;
+ if(child.level > mLevel) mLevel = child.level;
+ if(child.newickLen > mNewickLen) mNewickLen = child.newickLen;
+ if(child.children.length > 0){
+ recursiveProcessRoot(child, node);
+ }
+ }
+ }
+ return node;
+ },
+
+ recursiveProcessParameters = function(parametersEl, treeType){
+ for (var i in parametersEl){
+ if(i != '_children' && i != 'Text'){
+ if(i == 'rectangular' || i == 'circular'){
+ recursiveProcessParameters(parametersEl[i][0], i);
+ } else {
+ if(!Smits.PhyloCanvas.Render.Parameters[i]) { Smits.PhyloCanvas.Render.Parameters[i] = {}; };
+ Smits.PhyloCanvas.Render.Parameters.set(i, parametersEl[i][0].Text, treeType);
+ }
+ }
+ }
+ return;
+ };
+
+ return function(jsonString){
+ /* Privileged Methods */
+ this.getRoot = function(){
+ return root;
+ };
+ this.getLevels = function(){
+ return mLevel;
+ };
+ this.getNewickLen = function(){
+ return mNewickLen;
+ };
+ this.getValidate = function(){
+ return validate;
+ };
+
+
+ /* CONSTRUCTOR */
+ if(jsonString.phylogeny && jsonString.phylogeny[0] && jsonString.phylogeny[0].clade){
+ root = recursiveParse(jsonString.phylogeny[0].clade[0]);
+ }
+
+ if(jsonString.phylogeny && jsonString.phylogeny[0] && jsonString.phylogeny[0].render && jsonString.phylogeny[0].render[0]){
+ var render = jsonString.phylogeny[0].render[0];
+
+ // Custom Styles
+ if(render && render.styles){
+ var styles = render.styles[0];
+ for (var i in styles){
+ if(i != '_children' && i != 'Text'){
+ if(styles[i][0]['type'] && styles[i][0]['type'] == "radialGradient" && Raphael.svg){
+ // radialGradient only supported by SVG
+ styles[i][0]['name'] = i;
+ Smits.PhyloCanvas.Render.Style[i] = styles[i][0];
+ if(!Smits.PhyloCanvas.Render.Style['jsphylosvgGradientList']) { Smits.PhyloCanvas.Render.Style['jsphylosvgGradientList'] = [] };
+ Smits.PhyloCanvas.Render.Style['jsphylosvgGradientList'].push(i);
+ } else {
+ if(!Smits.PhyloCanvas.Render.Style[i]) { Smits.PhyloCanvas.Render.Style[i] = {}; };
+ for(var j in styles[i][0]){
+ if(j != '_attributes' && j != '_children' && j != 'type'){
+ Smits.PhyloCanvas.Render.Style[i][j.replace('_', '-')] = styles[i][0][j]; // This is quite painful, as xml does not allow dashes
+ }
+ }
+ }
+
+ }
+ }
+ }
+
+ // Custom Parameters
+ if(render && render.parameters){
+ recursiveProcessParameters(render.parameters[0]);
+ }
+
+ // Charts
+ if(render && render.charts){
+ var charts = render.charts[0];
+ for (var i in charts){
+ if(i != '_children' && i != 'Text'){
+ for(var j in charts[i]){
+ if(charts[i][j].type == "binary"){
+ charts[i][j].chart = i;
+ Smits.PhyloCanvas.Render.Parameters.binaryCharts.push(charts[i][j]);
+ } else if (charts[i][j].type == "integratedBinary"){
+ charts[i][j].chart = i;
+ Smits.PhyloCanvas.Render.Parameters.integratedBinaryCharts.push(charts[i][j]);
+ } else if (charts[i][j].type == "bar"){
+ charts[i][j].chart = i;
+ Smits.PhyloCanvas.Render.Parameters.barCharts.push(charts[i][j]);
+ }
+ }
+ }
+ }
+ }
+
+ }
+
+ root = recursiveProcessRoot(root);
+
+ }
+
+}();
+
+Smits.PhyloCanvas.PhyloxmlParse.prototype = {
+
+};Smits.PhyloCanvas.NexmlParse = function(){
+
+ var mLevel = 0,
+ mNewickLen = 0,
+ root,
+ validate,
+ nexEdges,
+ nexNodes,
+
+ recursiveParse = function(nexnode, nexlen, parentNode){
+ var node = new Smits.PhyloCanvas.Node();
+ if(parentNode){
+ node.level = parentNode.level + 1;
+ }
+
+ for(var i = 0; i < nexEdges.length; i++){
+ if(nexEdges[i].source == nexnode.id){
+ for(var j = 0; j < nexNodes.length; j++){
+ if(nexEdges[i].target == nexNodes[j].id){
+ node.children.push(recursiveParse(nexNodes[j], nexEdges[i].length, node));
+ }
+ }
+ }
+ }
+
+ if(nexlen) {
+ node.len = Smits.Common.roundFloat(nexlen, 4); // round to 4 decimal places
+ if(node.len == 0){
+ node.len = 0.0001;
+ }
+ }
+
+ if(nexnode.label){
+ node.type = 'label';
+ node.name = nexnode.label;
+ if(nexnode.style){
+ node.style = nexnode.style;
+ }
+ }
+
+
+ // Validation
+ if(node && node.level > 1){
+ if(!node.len){
+ validate = 'Error. Please include Branch Lengths - we only draw rooted phylogenetic trees.';
+ }
+ }
+
+ return node;
+ },
+
+ recursiveProcessRoot = function(node, parentNode){
+ if(node.children && node.children.length){
+ for( var i = 0; i < node.children.length; i++){
+ var child = node.children[i];
+ child.newickLen = Math.round( (child.len + node.newickLen) *10000)/10000;
+ if(child.level > mLevel) mLevel = child.level;
+ if(child.newickLen > mNewickLen) mNewickLen = child.newickLen;
+ if(child.children.length > 0){
+ recursiveProcessRoot(child, node);
+ }
+ }
+ }
+ return node;
+ },
+ recursiveProcessParameters = function(parametersEl, treeType){
+ for (var i in parametersEl){
+ if(i != '_children' && i != 'Text'){
+ if(i == 'rectangular' || i == 'circular'){
+ recursiveProcessParameters(parametersEl[i][0], i);
+ } else {
+ if(!Smits.PhyloCanvas.Render.Parameters[i]) { Smits.PhyloCanvas.Render.Parameters[i] = {}; };
+ Smits.PhyloCanvas.Render.Parameters.set(i, parametersEl[i][0].Text, treeType);
+ }
+ }
+ }
+ return;
+ };
+
+ return function(jsonString, inputFormat){
+ /* Privileged Methods */
+ this.getRoot = function(){
+ return root;
+ };
+ this.getLevels = function(){
+ return mLevel;
+ };
+ this.getNewickLen = function(){
+ return mNewickLen;
+ };
+ this.getValidate = function(){
+ return validate;
+ };
+
+
+ if(inputFormat.tree && jsonString.trees[0] && jsonString.trees[0].tree[(inputFormat.tree-1)]){
+ nexEdges = jsonString.trees[0].tree[(inputFormat.tree-1)].edge;
+ nexNodes = jsonString.trees[0].tree[(inputFormat.tree-1)].node;
+ } else {
+ nexEdges = jsonString.trees[0].tree[0].edge;
+ nexNodes = jsonString.trees[0].tree[0].node;
+ }
+
+ for(i = 0; i < nexNodes.length; i++){
+ if(nexNodes[i].root && nexNodes[i].root == "true"){
+ root = nexNodes[i];
+ }
+ }
+
+ if(root){
+ root = recursiveParse(root);
+
+ root = recursiveProcessRoot(root);
+ } else {
+ validate = 'Error. Currently, only rooted NeXML trees are supported.';
+ }
+
+ };
+
+}();
+
+Smits.PhyloCanvas.NexmlParse.prototype = {
+
+};Smits.PhyloCanvas.NexmlJsonParse = function(){
+
+ var mLevel = 0,
+ mNewickLen = 0,
+ root,
+ validate,
+ nexEdges = [], nexNodes = [],
+
+ recursiveParse = function(nexnode, nexlen, parentNode){
+ var node = new Smits.PhyloCanvas.Node();
+ if(parentNode){
+ node.level = parentNode.level + 1;
+ }
+
+ for(var i = 0; i < nexEdges.length; i++){
+ if(nexEdges[i].source == nexnode.id){
+ for(var j = 0; j < nexNodes.length; j++){
+ if(nexEdges[i].target == nexNodes[j].id){
+ node.children.push(recursiveParse(nexNodes[j], nexEdges[i].length, node));
+ }
+ }
+ }
+ }
+
+ if(nexlen) {
+ node.len = Smits.Common.roundFloat(nexlen, 4); // round to 4 decimal places
+ if(node.len == 0){
+ node.len = 0.0001;
+ }
+ }
+
+ if(nexnode.label){
+ node.type = 'label';
+ node.name = nexnode.label;
+ if(nexnode.accession){
+ node.accession = nexnode.accession;
+ }
+ if(nexnode.style){
+ node.style = nexnode.style;
+ }
+ if(nexnode.bgStyle){
+ node.bgStyle = nexnode.bgStyle;
+ }
+ }
+
+ if(nexnode.chart){
+ node.chart = nexnode.chart;
+ }
+
+ // Validation
+ if(node && node.level > 1){
+ if(!node.len){
+ validate = 'Error. Please include Branch Lengths - we only draw rooted phylogenetic trees.';
+ }
+ }
+
+ return node;
+ },
+
+ recursiveProcessRoot = function(node, parentNode){
+ if(node.children && node.children.length){
+ for( var i = 0; i < node.children.length; i++){
+ var child = node.children[i];
+ child.newickLen = Math.round( (child.len + node.newickLen) *10000)/10000;
+ if(child.level > mLevel) mLevel = child.level;
+ if(child.newickLen > mNewickLen) mNewickLen = child.newickLen;
+ if(child.children.length > 0){
+ recursiveProcessRoot(child, node);
+ }
+ }
+ }
+ return node;
+ },
+
+ recursiveProcessParameters = function(parametersEl, treeType){
+ for (var i in parametersEl){
+ if(i != '_children' && i != 'Text'){
+ if(i == 'rectangular' || i == 'circular'){
+ recursiveProcessParameters(parametersEl[i], i);
+ } else {
+ if(!Smits.PhyloCanvas.Render.Parameters[i]) { Smits.PhyloCanvas.Render.Parameters[i] = {}; };
+ Smits.PhyloCanvas.Render.Parameters.set(i, parametersEl[i], treeType);
+ }
+ }
+ }
+ return;
+ };
+
+ return function(inputFormat){
+ /* Privileged Methods */
+ this.getRoot = function(){
+ return root;
+ };
+ this.getLevels = function(){
+ return mLevel;
+ };
+ this.getNewickLen = function(){
+ return mNewickLen;
+ };
+ this.getValidate = function(){
+ return validate;
+ };
+
+ var jsonString = inputFormat.nexmlJson.nexml;
+
+
+ /* RENDER STYLES */
+ var render = jsonString.render;
+
+ // Custom Styles
+ if(render && render.styles){
+ var styles = render.styles;
+ for (var i in styles){
+ if(i != '_children' && i != 'Text'){
+ if(styles[i]['@attributes']['type'] && styles[i]['@attributes']['type'] == "radialGradient" && Raphael.svg){
+ // radialGradient only supported by SVG
+ styles[i]['name'] = i;
+ styles[i]['type'] = styles[i]['@attributes']['type'];
+ Smits.PhyloCanvas.Render.Style[i] = styles[i];
+ if(!Smits.PhyloCanvas.Render.Style['jsphylosvgGradientList']) { Smits.PhyloCanvas.Render.Style['jsphylosvgGradientList'] = [] };
+ Smits.PhyloCanvas.Render.Style['jsphylosvgGradientList'].push(i);
+ } else {
+ if(!Smits.PhyloCanvas.Render.Style[i]) { Smits.PhyloCanvas.Render.Style[i] = {}; };
+ for(var j in styles[i]['@attributes']){
+ if(j != '_attributes' && j != '_children' && j != 'type'){
+ Smits.PhyloCanvas.Render.Style[i][j.replace('_', '-')] = styles[i]['@attributes'][j]; // This is quite painful, as xml does not allow dashes
+ }
+ }
+ }
+ }
+ }
+ }
+ // Custom Parameters
+ if(render && render.parameters){
+ recursiveProcessParameters(render.parameters);
+ }
+
+ // Charts
+ if(render && render.charts){
+ var charts = render.charts;
+ for (var i in charts){
+ charts[i]['@attributes'].chart = i;
+ if(charts[i]['@attributes'].type == "binary"){
+ Smits.PhyloCanvas.Render.Parameters.binaryCharts.push(charts[i]['@attributes']);
+ } else if(charts[i]['@attributes'].type == "integratedBinary"){
+ Smits.PhyloCanvas.Render.Parameters.integratedBinaryCharts.push(charts[i]['@attributes']);
+ } else if(charts[i]['@attributes'].type == "bar"){
+ Smits.PhyloCanvas.Render.Parameters.barCharts.push(charts[i]['@attributes']);
+ }
+ }
+ }
+
+ if(inputFormat.tree && jsonString.trees[0] && jsonString.trees[0].tree[(inputFormat.tree-1)]){
+ nexEdges = jsonString.trees[0].tree[(inputFormat.tree-1)].edge;
+ nexNodes = jsonString.trees[0].tree[(inputFormat.tree-1)].node;
+ } else {
+ for(var i = 0; i < jsonString.trees.tree.edge.length; i++){
+ nexEdges.push(jsonString.trees.tree.edge[i]['@attributes']);
+ }
+ for(var i = 0; i < jsonString.trees.tree.node.length; i++){
+ var node = jsonString.trees.tree.node[i]['@attributes'];
+ if(node.label){
+ node.chart = jsonString.trees.tree.node[i].chart;
+ }
+ nexNodes.push(node);
+ }
+ }
+
+ for(var i = 0; i < nexNodes.length; i++){
+ if(nexNodes[i].root && nexNodes[i].root == "true"){
+ root = nexNodes[i];
+ }
+ }
+
+ if(root){
+ root = recursiveParse(root);
+
+ root = recursiveProcessRoot(root);
+ } else {
+ validate = 'Error. Currently, only rooted NeXML trees are supported.';
+ }
+
+ };
+
+}();
+
+Smits.PhyloCanvas.NexmlParse.prototype = {
+
+};Smits.PhyloCanvas.Render = {};Smits.PhyloCanvas.Render.Style = {
+
+ /* Default Styles */
+
+ line: {
+ "stroke": 'rgb(0,0,0)',
+ "stroke-width": 1
+ },
+
+ text: {
+ "font-family": 'Verdana',
+ "font-size": 12,
+ "text-anchor": 'start'
+ },
+
+ path: {
+ "stroke": 'rgb(0,0,0)',
+ "stroke-width": 1
+ },
+
+ connectedDash : {
+ "stroke": 'rgb(200,200,200)',
+ "stroke-dasharray": ". "
+ },
+
+ textSecantBg : {
+ "fill": '#EEE',
+ "stroke": '#DDD'
+ },
+
+ highlightedEdgeCircle : {
+ "fill": 'red'
+ },
+
+ barChart : {
+ fill: '#003300',
+ stroke: '#DDD'
+ },
+
+ getStyle : function(requestStyle, fallbackStyle){
+ if...
[truncated message content] |
|
From: SourceForge.net <no...@so...> - 2011-05-17 15:40:36
|
Bugs item #3303390, was opened at 2011-05-17 11:40 Message generated for change (Tracker Item Submitted) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3303390&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None Status: Open Priority: 8 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: hshyket (hshyket) Summary: Some tree newicks do not end in semi-colons Initial Comment: It appears that when TreeBASE downloads trees, the newick string is pulled straight from the "newickstring" field in the phylotree table, instead of being reconstructed on the fly using the nodes and edges. Some of these trees are missing a semi-colon at the end of the newickstring. For example, in study S10830, tree Tr25629 is missing a semi-colon, while tree Tr25630 is not missing the semi-colon. The missing semi-colon can happen as a result of rerooting the tree using PhyloWidget and then saving the new rerooted tree back to the "newickstring" field. But however this creeps in, whenever trees are written, we should check to add a semi-colon to the end of the newick string. For example, all these links end up creating trees in newick, and in each case they are missing the semi-colon for Tr25629: http://www.treebase.org/treebase-web/phylows/tree/TB2:Tr25629?format=nexus http://www.treebase.org/treebase-web/search/downloadAnAnalysisStep.html?analysisid=6642&id=10830 http://www.treebase.org/treebase-web/search/downloadATree.html?id=10830&treeid=25629 http://www.treebase.org/treebase-web/tree_for_phylowidget/TB2:Tr25629 http://purl.org/phylo/treebase/phylows/study/TB2:S10830?format=nexus ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3303390&group_id=248804 |
|
From: SourceForge.net <no...@so...> - 2011-05-17 14:31:01
|
Bugs item #3303346, was opened at 2011-05-17 10:30 Message generated for change (Tracker Item Submitted) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3303346&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None Status: Open Priority: 9 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: hshyket (hshyket) Summary: Tracking Usage Statistics Initial Comment: We need a mechanism for tracking usage (e.g. how often people search the database, how often a tree, matrix, or analysis is downloaded), possibly collecting other data like IP origin. Finding a solution to for this might be complicated by the fact that we ask robots not to scrape TreeBASE. I put this as a high priority because we need to start collecting this data soon in anticipation of applying for new funding. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3303346&group_id=248804 |
|
From: SourceForge.net <no...@so...> - 2011-05-17 01:09:28
|
Bugs item #3303076, was opened at 2011-05-16 21:09 Message generated for change (Tracker Item Submitted) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3303076&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None Status: Open Priority: 7 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: hshyket (hshyket) Summary: Search on ISO 8601 date styles Initial Comment: Currently, the API allows the user to search by date, e.g.: http://treebase-dev.nescent.org/treebase-web/phylows/study/find?query=prism.creationDate>"May 5, 2011"&format=rss1 http://treebase-dev.nescent.org/treebase-web/phylows/study/find?query=prism.modificationDate>"May 5, 2011"&format=rss1 http://treebase-dev.nescent.org/treebase-web/phylows/study/find?query=prism.publicationDate>"May 5, 2011"&format=rss1 However, CQL usually expects the date format to conform to ISO 8601: http://www.loc.gov/standards/sru/resources/cql-context-set-v1-2.html This date style already works for our OAI-PMH service, e.g.: http://treebase.org/treebase-web/top/oai?verb=ListRecords&metadataPrefix=oai_dc&from=2011-05-05T00:00:00Z Let's expand the date format in the API -- if anything it avoids needing to put the date in quotes. The issue is to configure the DateFormat object correctly which is done in the StudySearchController, at lines 311, 332 and 350. You can probably pass date formatting templates to the factory that returns a date parser through the getInstance() call. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3303076&group_id=248804 |
|
From: SourceForge.net <no...@so...> - 2011-05-16 19:48:42
|
Bugs item #3303006, was opened at 2011-05-16 15:48 Message generated for change (Tracker Item Submitted) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3303006&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None Status: Open Priority: 6 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: hshyket (hshyket) Summary: Delete tree warned that tree is part of analysis Initial Comment: When a submitter tries to delete a tree block, a warning message in red text tells the submitter that the tree he/she is deleting is participating in an analysis. This is a useful warning, but the warning happens whether or not any of the trees in the tree block are actually linked to an analysis or not. Either fix the warning or remove the warning. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3303006&group_id=248804 |
|
From: SourceForge.net <no...@so...> - 2011-05-16 19:46:14
|
Bugs item #3303002, was opened at 2011-05-16 15:46 Message generated for change (Tracker Item Submitted) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3303002&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None Status: Open Priority: 8 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: hshyket (hshyket) Summary: NeXML not working for matrix or tree Initial Comment: Downloading NeXML works for the whole study, e.g.: http://purl.org/phylo/treebase/phylows/study/TB2:S586?format=nexml But does not seem to work for matrices in this study, e.g.: http://purl.org/phylo/treebase/phylows/matrix/TB2:M2225?format=nexml Or trees in this study: http://www.treebase.org/treebase-web/phylows/tree/TB2:Tr3535?format=nexml ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3303002&group_id=248804 |
|
From: SourceForge.net <no...@so...> - 2011-05-16 19:43:39
|
Bugs item #3302998, was opened at 2011-05-16 15:43 Message generated for change (Tracker Item Submitted) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3302998&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None Status: Open Priority: 7 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: hshyket (hshyket) Summary: Dryad data DOI number storage Initial Comment: When a submission is pushed on to TreeBASE from Dryad, by default the "Study Name" is pre-populated with the Dryad number in the form of "dryad_7877" and the "Study Notes" is pre-populated with the list of authors & instructions about retyping the authors in. Let's change this so that the "dryad_7877" number is prefixed in the Study Notes section and so that the title of the paper is pre-populated into the "Study Name" area. Also, let's pre-populate the URL field of the citation with the fully resolvable Dryad Package Identifier, e.g. http://dx.doi.org/10.5061/dryad.7877. When it comes to exposing this URL field, let's do the following: (1) if the URL field is shorter than 8 letters, don't expose it. (2) if the URL field starts with anything other than "http://dx.doi.org", expose it with the element or property "prism:url" (3) if the URL field starts with "http://dx.doi.org", expose it with the element or property "dcterms:isPartOf" The places where the URL field is exposed is essentially the same places where the publication DOI gets exposed, e.g.: - the RDF serialization of a study (e.g. http://purl.org/phylo/treebase/dev/phylows/study/TB2:S586?format=rdf) - the NeXML serialization of a study (e.g. http://purl.org/phylo/treebase/dev/phylows/study/TB2:S586?format=nexml) - the OAI-PMH return (e.g. http://treebase.org/treebase-web/top/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier=TB:s586) ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3302998&group_id=248804 |
|
From: SourceForge.net <no...@so...> - 2011-05-16 19:16:27
|
Bugs item #3302987, was opened at 2011-05-16 15:16 Message generated for change (Tracker Item Submitted) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3302987&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None Status: Open Priority: 7 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: hshyket (hshyket) Summary: Discard All Results button does not work after phylows query Initial Comment: If a user uses /phylows/ to create a selection of records in the html presentation, the selection cannot be cleared by pressing the "Discard All Results" button. For example: http://treebase-dev.nescent.org/treebase-web/search/studySearch.html?query=prism.creationDate%3E%22May%205,%202011%22 The only way to clear it is to select another tab, and then press the Discard All Results button. This problem does not happen if the selection is made as a result of the same search performed with the GUI. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3302987&group_id=248804 |
|
From: SourceForge.net <no...@so...> - 2011-05-16 19:11:40
|
Bugs item #3302986, was opened at 2011-05-16 15:11 Message generated for change (Tracker Item Submitted) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3302986&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None Status: Open Priority: 7 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: hshyket (hshyket) Summary: Study Search crowded with buttons Initial Comment: The study search is crowded with buttons ("Study ID" "Legacy Study ID" "Author" "Title" "Abstract" and "Entire Citation" "All test"). Instead of having separate buttons, could we have a dropdown or popup list for these things plus a "Search" button. This will be especially needed when the prism.publicationDate, prism.modificationDate, and prism.creationDate search terms are introduced (per Revision: 844, http://treebase.svn.sourceforge.net/treebase/?rev=844&view=rev). It would be best if the default item in the dropdown is set to whatever was last used by the user in the session. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3302986&group_id=248804 |
|
From: SourceForge.net <no...@so...> - 2011-05-16 18:27:27
|
Bugs item #3300808, was opened at 2011-05-11 23:08 Message generated for change (Settings changed) made by sfrgpiel You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3300808&group_id=248804 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: ui Group: None >Status: Closed Priority: 7 Private: No Submitted By: William Piel (sfrgpiel) Assigned to: hshyket (hshyket) Summary: Submission notes can break javascript Initial Comment: Sometimes the yellow highlights do not show up on Tool Box items that have errors or have not been visited. Often editing the submission notes field solves the problem -- it looks as though extra return keys in the text are responsible for the problem. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1126676&aid=3300808&group_id=248804 |
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From: <rv...@us...> - 2011-05-16 16:38:57
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Revision: 868
http://treebase.svn.sourceforge.net/treebase/?rev=868&view=rev
Author: rvos
Date: 2011-05-16 16:38:51 +0000 (Mon, 16 May 2011)
Log Message:
-----------
It is better to use an onclick handler than the javascript: pseudo protocol. Also removed some of the styling. We'll make it look pretty once tree drawing works.
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/limitedPhylowidget.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/limitedPhylowidget.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/limitedPhylowidget.jsp 2011-05-13 14:32:50 UTC (rev 867)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/limitedPhylowidget.jsp 2011-05-16 16:38:51 UTC (rev 868)
@@ -52,9 +52,7 @@
fieldset {
display:block;
- background:#CEE3F6;
margin:auto;
- text-align:center;
}
legend {
@@ -91,13 +89,7 @@
<legend>Tree window</legend>
<script type="text/javascript">
function drawjsPhyloSVGTree(namespacedGUID,ntax){
- var uri = "/treebase-web/phylows/tree/";
- if ( null != namespacedGUID ) {
- uri = uri + namespacedGUID + "?format=nexml";
- }
- else {
- uri = uri + document.TreeForm.treeList.value + "?format=nexml";
- }
+ var uri = "/treebase-web/phylows/tree/" + namespacedGUID + "?format=nexml";
new Ajax.Request(uri,{
method : 'get',
onComplete : function(transport) {
@@ -108,7 +100,7 @@
phylocanvas = new Smits.PhyloCanvas(
dataObject,
'svgCanvas',
- 600, 600
+ 600, ntax * 20
);
},
onFailure: function(){
@@ -117,40 +109,30 @@
});
};
</script>
- <div id="svgCanvas" style="width:600px;height:600px"></div>
+ <div id="svgCanvas" style="width:600px"></div>
</fieldset>
</td>
<td style="vertical-align:top">
- <fieldset style="margin-top:10px;margin-left:5px;margin-right:5px">
+ <fieldset>
<legend><c:out value="${NEWICKSTRINGNAME}"/></legend>
- <select
- name="treeList"
- size="10"
- onclick="javascript:drawjsPhyloSVGTree();"
- id="treeList">
- <c:forEach var="x" items="${PHYLOWSMAP}">
- <option value="${x.value}">${x.key}</option>
- </c:forEach>
- </select>
<ol>
<c:forEach var="tree" items="${TREELIST}">
- <li>
- <a href="javascript:drawjsPhyloSVGTree(${tree.treebaseIDString.namespacedGUID},${tree.nTax})">${tree.label} ${tree.title}</a>
+ <li onclick="drawjsPhyloSVGTree('${tree.treebaseIDString.namespacedGUID}',${tree.nTax})">
+ ${tree.label} ${tree.title}
</li>
- <option value="${x.value}">${x.key}</option>
</c:forEach>
</ol>
</fieldset>
<c:if test="${treeBlockID != null}">
- <fieldset style="margin-left:5px;margin-right:5px;background-color:white">
+ <fieldset>
<legend>Quick links</legend>
- <p style="text-align:left">
+ <p>
<a href="/treebase-web/search/study/trees.html?id=${studyID}" target="_new">
<img class="iconButton" style="vertical-align:middle" src="<fmt:message key="icons.trees"/>" />
Containing tree set
</a>
</p>
- <p style="text-align:left">
+ <p>
<a href="/treebase-web/search/study/summary.html?id=${studyID}" target="_new">
<img class="iconButton" style="vertical-align:middle" src="<fmt:message key="icons.citation"/>" />
Containing study
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From: <hs...@us...> - 2011-05-13 14:32:56
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Revision: 867
http://treebase.svn.sourceforge.net/treebase/?rev=867&view=rev
Author: hshyket
Date: 2011-05-13 14:32:50 +0000 (Fri, 13 May 2011)
Log Message:
-----------
Fixing issue where Javascript was broken when JSON data had line breaks in it. Encoded the line breaks to characters.
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/json/studyToJSON.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/json/studyToJSON.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/json/studyToJSON.jsp 2011-05-12 22:49:40 UTC (rev 866)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/json/studyToJSON.jsp 2011-05-13 14:32:50 UTC (rev 867)
@@ -2,7 +2,15 @@
{
id:${study.id},
name:'<c:out value="${study.name}"/>',
-notes:'<c:out value="${study.notes}"/>',
+<% pageContext.setAttribute("returnLineChar", "\r"); %>
+<% pageContext.setAttribute("newLineChar", "\n"); %>
+<c:set var="notes">
+ ${fn:replace(study.notes,returnLineChar, "\\r")}
+</c:set>
+<c:set var="notes">
+ ${fn:replace(notes,newLineChar, "\\n")}
+</c:set>
+notes:'<c:out value="${notes}"/>',
authors:[<c:forEach var="author" items="${study.authors}" varStatus="status_analysis">
{id:${author.id},fullNameCitationStyle:'<c:out value="${author.fullNameCitationStyle}"/>'},
</c:forEach>],
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From: <rv...@us...> - 2011-05-12 22:49:46
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Revision: 866
http://treebase.svn.sourceforge.net/treebase/?rev=866&view=rev
Author: rvos
Date: 2011-05-12 22:49:40 +0000 (Thu, 12 May 2011)
Log Message:
-----------
using tree list to create links
Modified Paths:
--------------
trunk/treebase-web/src/main/webapp/WEB-INF/pages/limitedPhylowidget.jsp
Modified: trunk/treebase-web/src/main/webapp/WEB-INF/pages/limitedPhylowidget.jsp
===================================================================
--- trunk/treebase-web/src/main/webapp/WEB-INF/pages/limitedPhylowidget.jsp 2011-05-12 22:49:08 UTC (rev 865)
+++ trunk/treebase-web/src/main/webapp/WEB-INF/pages/limitedPhylowidget.jsp 2011-05-12 22:49:40 UTC (rev 866)
@@ -8,8 +8,6 @@
<title>-Tree viewer</title>
<script type="text/javascript" src="<c:url value='/scripts/prototype/prototype-1.6.0.3.js'/>"></script>
-<!-- script type="text/javascript" src="<c:url value='/scripts/phylowidget/lib.js'/>"></script-->
-<!-- script type="text/javascript" src="<c:url value='/scripts/phylowidget.js'/>"></script-->
<script type="text/javascript" src="<c:url value='/scripts/raphael-min.js'/>"></script>
<script type="text/javascript" src="<c:url value='/scripts/jsphylosvg-min.js'/>"></script>
@@ -85,64 +83,21 @@
</style>
</head>
<body>
- <!-- script type="text/javascript">
- TreeBASE.register(
- function () {
- var treeList = $('treeList');
- var option = treeList.select('option');
- var treeText = $('treeText');
- treeText.value = option[0].value;
- updateJavaTree();
- }
- );
- </script -->
<form name="TreeForm">
<table id="content" style="margin-top: 5px">
<tr>
<td style="vertical-align:top">
- <%-- fieldset>
- <legend>PhyloWidget
-<a href="#" class="openHelp" onclick="openHelp('newPhyloWidget')"><img class="iconButton" src="<fmt:message key="icons.help"/>" /></a>
- </legend>
- <applet
- code="org.phylowidget.PhyloWidget"
- id="PhyloWidget"
- name="PhyloWidget"
- codebase="./phylowidget"
- archive="PhyloWidget.jar,core.jar,itext.jar,jgrapht-jdk1.5.jar,pdf.jar"
- mayscript="true"
- width="600" height="600">
- <param name="tree" value="<c:out value="${DEFAULTNEWICK}"/>"/>
-
-
- <!--
- Additional parameters can be passed to the widget, which
- are parsed out by PhyloUI.java, e.g.:
- <param name="showBranchLengths" value="true"/>
- <param name="useBranchLengths" value="true"/>
- -->
- <param name="menuFile" value="limited-menus.xml" />
- <param name="image" value="loading.gif" />
- <param name="boxmessage" value="Loading PhyloWidget software..." />
- <param name="boxbgcolor" value="#FFFFFF" />
- <param name="progressbar" value="true" />
- <param name="subapplet.classname" value="org.phylowidget.PhyloWidget" />
- <param name="subapplet.displayname" value="PhyloWidget" />
- <param name="cache_archive" value="PhyloWidget.jar,core.jar,itext.jar,jgrapht-jdk1.5.jar,pdf.jar"/>
- <param name="cache_archive_ex" value="PhyloWidget.jar;preload,core.jar;preload,itext.jar;preload,jgrapht-jdk1.5.jar;preload,pdf.jar;preload"/>
-
-
- <!-- This is the message that shows up when people don't have
- Java installed in their browser. -->
- To view this content, you need to install Java from
- <a href="http://java.com">java.com</a>
- </applet>
- </fieldset --%>
<fieldset>
<legend>Tree window</legend>
<script type="text/javascript">
- function drawjsPhyloSVGTree(){
- var uri = "/treebase-web/phylows/tree/"+document.TreeForm.treeList.value+"?format=nexml";
+ function drawjsPhyloSVGTree(namespacedGUID,ntax){
+ var uri = "/treebase-web/phylows/tree/";
+ if ( null != namespacedGUID ) {
+ uri = uri + namespacedGUID + "?format=nexml";
+ }
+ else {
+ uri = uri + document.TreeForm.treeList.value + "?format=nexml";
+ }
new Ajax.Request(uri,{
method : 'get',
onComplete : function(transport) {
@@ -165,15 +120,7 @@
<div id="svgCanvas" style="width:600px;height:600px"></div>
</fieldset>
</td>
- <td style="vertical-align:top">
- <fieldset style="margin-left:5px;margin-right:5px">
- <legend>Node Info</legend>
- <div id="nodeText" style="background:white;margin:5px;padding:5px;">
- Mouse over a node to view its detailed information here.
- Node details will be displayed if they were described in
- the uploaded tree.
- </div>
- </fieldset>
+ <td style="vertical-align:top">
<fieldset style="margin-top:10px;margin-left:5px;margin-right:5px">
<legend><c:out value="${NEWICKSTRINGNAME}"/></legend>
<select
@@ -181,29 +128,19 @@
size="10"
onclick="javascript:drawjsPhyloSVGTree();"
id="treeList">
- <%--c:forEach var="x" items="${NEWICKSTRINGSMAP}" >
- <option value="${x.value}">${x.key}</option>
- </c:forEach --%>
<c:forEach var="x" items="${PHYLOWSMAP}">
<option value="${x.value}">${x.key}</option>
</c:forEach>
</select>
+ <ol>
+ <c:forEach var="tree" items="${TREELIST}">
+ <li>
+ <a href="javascript:drawjsPhyloSVGTree(${tree.treebaseIDString.namespacedGUID},${tree.nTax})">${tree.label} ${tree.title}</a>
+ </li>
+ <option value="${x.value}">${x.key}</option>
+ </c:forEach>
+ </ol>
</fieldset>
- <!-- input
- type="hidden"
- name="treeText"
- id="treeText"
- onfocus="selectOnce(this);"
- value="" />
- <input
- type="hidden"
- name="clipText"
- id="clipText"
- onchange="updateJavaClip();"
- value="" /-->
- <div id="comments" style="margin: 5px">
- Make a selection by clicking on the tree list.
- </div>
<c:if test="${treeBlockID != null}">
<fieldset style="margin-left:5px;margin-right:5px;background-color:white">
<legend>Quick links</legend>
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From: <rv...@us...> - 2011-05-12 22:49:16
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Revision: 865
http://treebase.svn.sourceforge.net/treebase/?rev=865&view=rev
Author: rvos
Date: 2011-05-12 22:49:08 +0000 (Thu, 12 May 2011)
Log Message:
-----------
Adding tree list as session attribute
Modified Paths:
--------------
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DirectMapToPhyloWidgetController.java
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DirectMapToPhyloWidgetController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DirectMapToPhyloWidgetController.java 2011-05-12 20:42:36 UTC (rev 864)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/DirectMapToPhyloWidgetController.java 2011-05-12 22:49:08 UTC (rev 865)
@@ -1,6 +1,8 @@
package org.cipres.treebase.web.controllers;
+import java.util.ArrayList;
import java.util.HashMap;
+import java.util.List;
import org.apache.log4j.Logger;
import java.util.Map;
@@ -54,6 +56,7 @@
String separator = "@";
Map<String, String> treeMap = new HashMap<String, String>();
Map<String,String> phylowsMap = new HashMap<String,String>();
+ List<PhyloTree> treeList = new ArrayList<PhyloTree>();
String newickStringName = null;
if (pRequest.getParameter("treeblockid") != null) {
@@ -76,6 +79,7 @@
if ( defaultNewick.equals("") ) {
defaultNewick = aTree.getNewickString();
}
+ treeList.add(aTree);
}
// XXX ok, so this mess started when we somehow combined phylowidget for searching
// with phylowidget for submission (why???) -- rvosa
@@ -94,6 +98,7 @@
String TreeId = pRequest.getParameter("treeid");
PhyloTree aTree = getPhyloTreeService().findByID(Long.parseLong(TreeId));
+ treeList.add(aTree);
// use "T" to enable the edit menu items.
treeMap.put(getMapKey(aTree), TreeId + separator + aTree.getNewickString() + separator
@@ -112,6 +117,7 @@
pRequest.getSession().setAttribute("NEWICKSTRINGSMAP", treeMap);
pRequest.getSession().setAttribute("PHYLOWSMAP", phylowsMap);
pRequest.getSession().setAttribute("NEWICKSTRINGNAME", newickStringName);
+ pRequest.getSession().setAttribute("TREELIST", treeList);
return new ModelAndView(getDefaultView());
}
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