3 PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
4 <html xmlns="http://www.w3.org/1999/xhtml">
6 <title>Documentation for phyloXML 1.00 - phyloxml.xsd</title>
7 <meta http-equiv="Content-Type" content="text/xml; charset=UTF-8"/>
8 <style type="text/css">
9 /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */
10 /* More-configurable styles */
12 /******** General ********/
17 background-color: White;
18 font-family: Arial, sans-serif;
22 /* Horizontal rules */
30 border-bottom: 1px #ccc solid;
34 /* Main section headers */
39 /* Sub-section headers */
45 /* Table displaying the properties of the schema components or the
46 schema document itself */
47 table.properties th, table.properties th a {
49 background-color: #F99; /* Pink */
52 background-color: #eee; /* Gray */
59 /********* Documentation style *************/
63 background-color: #EEEEFF;
64 border: 1px solid #DDDDFF;
71 /******** Table of Contents Section ********/
73 /* Controls for switching between printing and viewing modes */
75 color: #963; /* Orange-brown */
77 /* Controls that can collapse or expand all XML Instance
78 Representation and Schema Component Representation boxes */
80 border: 2px solid #999;
84 /******** Schema Document Properties Section ********/
86 /* Table displaying the namespaces declared in the schema */
88 background-color: #ccc;
91 background-color: #eee;
93 /* Target namespace of the schema */
100 /******** Schema Components' Sections ********/
102 /* Name of schema component */
104 color: #F93; /* Orange */
107 /* Hierarchy table */
109 border: 2px solid #999; /* Gray */
112 /* XML Instance Representation table */
113 div.sample div.contents {
114 border: 1px dashed black;
118 /* Schema Component Representation table */
119 div.schemaComponent div.contents {
120 border: 2px black solid;
124 /******** Glossary Section ********/
128 color: #036; /* Blue */
132 /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */
133 /* Printer-version styles */
137 /* Ensures that controls are hidden when printing */
138 div#printerControls {
159 /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */
162 /******** General ********/
164 /* Unordered lists */
188 /* Table displaying the properties of the schema components or the
189 schema document itself */
193 table.properties th {
196 /* Boxes that can make its content appear and disappear*/
201 div.box span.caption {
204 /* Button to open and close the box */
205 div.box input.control {
209 vertical-align: middle;
213 div.box div.contents {
218 /******** Table of Contents Section ********/
220 /* Controls for switching between printing and viewing modes */
221 div#printerControls {
227 /* Controls that can collapse or expand all XML Instance
228 Representation and Schema Component Representation boxes */
235 /******** Schema Document Properties Section ********/
237 /* Table displaying the namespaces declared in the schema */
238 table.namespaces th {
240 table.namespaces td {
242 /* Target namespace of the schema */
247 /******** Schema Components' Sections ********/
249 /* Name of schema component */
253 /* Hierarchy table */
262 table.hierarchy th, table.hierarchy td {
266 /* XML Instance Representation table */
270 div.sample div.contents {
272 font-family: Courier New, sans-serif;
275 /* Normal elements and attributes */
276 div.sample div.contents, div.sample div.contents a {
280 div.sample div.contents .group, div.sample div.contents .group a {
281 color: #999; /* Light gray */
283 /* Type Information */
284 div.sample div.contents .type, div.sample div.contents .type a {
285 color: #999; /* Light gray */
287 /* Occurrence Information */
288 div.sample div.contents .occurs, div.sample div.contents .occurs a {
289 color: #999; /* Light gray */
292 div.sample div.contents .fixed {
293 color: #063; /* Green */
296 /* Simple type constraints */
297 div.sample div.contents .constraint, div.sample div.contents .constraint a {
298 color: #999; /* Light gray */
300 /* Elements and attributes inherited from base type */
301 div.sample div.contents .inherited, div.sample div.contents .inherited a {
302 color: #666; /* Dark gray */
304 /* Elements and attributes added to or changed from base type */
305 div.sample div.contents .newFields {
308 /* Other type of information */
309 div.sample div.contents .other, div.sample div.contents .other a {
310 color: #369; /* Blue */
313 /* Link to open up window displaying documentation */
314 div.sample div.contents a.documentation {
315 text-decoration: none;
322 background-color: #FFD;
325 /* Invert colors when hovering over link to open up window
326 displaying documentation */
327 div.sample div.contents a.documentation:hover {
329 background-color: #069;
332 /* Schema Component Representation table */
333 div.schemaComponent {
336 div.schemaComponent div.contents {
337 font-family: Courier New, sans-serif;
341 /* Syntax characters */
342 div.schemaComponent div.contents {
343 color: #00f; /* blue */
345 /* Element and attribute tags */
346 div.schemaComponent div.contents .scTag {
347 color: #933; /* maroon */
349 /* Element and attribute content */
350 div.schemaComponent div.contents .scContent, div.schemaComponent div.contents .scContent a {
355 div.schemaComponent div.contents .comment {
356 color: #999; /* Light gray */
359 /******** Legend Section ********/
361 div#legend table, div#legend div {
364 div#legend div.hint {
365 color: #999; /* Light gray */
372 /******** Glossary Section ********/
379 /********* Details *************/
381 color: #666; /* Light gray */
385 color: #666; /* Light gray */
386 text-decoration:none;
389 /******** Footer ********/
395 <script type="text/javascript">
397 /* IDs of XML Instance Representation boxes */
398 var xiBoxes = new Array('h270234806_xibox', 'h155831896_xibox', 'h535307528_xibox', 'h-1124608460_xibox', 'h888650454_xibox', 'h712147427_xibox', 'h518348337_xibox', 'h-1794244794_xibox', 'h-213750342_xibox', 'h935679102_xibox', 'h1408823200_xibox', 'h-788356801_xibox', 'h259010940_xibox', 'h-1389097534_xibox', 'h-436501026_xibox', 'h1358103055_xibox', 'h-1514309680_xibox', 'h1535743041_xibox', 'h401516646_xibox', 'h-676028775_xibox', 'h917087604_xibox', 'h158033242_xibox', 'h-675984882_xibox', 'h-763252414_xibox', 'h-54338178_xibox', 'h-676012345_xibox', 'h-993584945_xibox', 'h-853091232_xibox', 'h-979596407_xibox', 'h-1112505301_xibox', 'h332351765_xibox', 'h517931443_xibox', 'h-1691165380_xibox', 'h-802965662_xibox', 'h519911868_xibox', 'h192331856_xibox', 'h-1482113798_xibox', 'h577349652_xibox');
399 /* IDs of diagram boxes */
400 var diagramBoxes = new Array('h270234806_diagram', 'h155831896_diagram', 'h535307528_diagram', 'h-1124608460_diagram', 'h888650454_diagram', 'h712147427_diagram', 'h518348337_diagram', 'h-1794244794_diagram', 'h-213750342_diagram', 'h935679102_diagram', 'h1408823200_diagram', 'h-788356801_diagram', 'h259010940_diagram', 'h-1389097534_diagram', 'h-436501026_diagram', 'h1358103055_diagram', 'h-1514309680_diagram', 'h1535743041_diagram', 'h401516646_diagram', 'h-676028775_diagram', 'h917087604_diagram', 'h158033242_diagram', 'h-675984882_diagram', 'h-763252414_diagram', 'h-54338178_diagram', 'h-676012345_diagram', 'h-993584945_diagram', 'h-853091232_diagram', 'h-979596407_diagram', 'h-1112505301_diagram', 'h332351765_diagram', 'h517931443_diagram', 'h-1691165380_diagram', 'h-802965662_diagram', 'h519911868_diagram', 'h192331856_diagram', 'h-1482113798_diagram', 'h577349652_diagram');
401 /* IDs of logical diagram boxes */
402 var logicalDiagramBoxes = new Array('h270234806_logicalDiagram');
403 /* IDs of Schema Component Representation boxes */
404 var scBoxes = new Array('schema_scbox', 'h270234806_scbox', 'h155831896_scbox', 'h535307528_scbox', 'h-1124608460_scbox', 'h888650454_scbox', 'h712147427_scbox', 'h518348337_scbox', 'h-1794244794_scbox', 'h-213750342_scbox', 'h935679102_scbox', 'h1408823200_scbox', 'h-788356801_scbox', 'h259010940_scbox', 'h-1389097534_scbox', 'h-436501026_scbox', 'h1358103055_scbox', 'h-1514309680_scbox', 'h1535743041_scbox', 'h401516646_scbox', 'h-676028775_scbox', 'h917087604_scbox', 'h158033242_scbox', 'h-675984882_scbox', 'h-763252414_scbox', 'h-54338178_scbox', 'h-676012345_scbox', 'h-993584945_scbox', 'h-853091232_scbox', 'h-979596407_scbox', 'h-1112505301_scbox', 'h332351765_scbox', 'h517931443_scbox', 'h-1691165380_scbox', 'h-802965662_scbox', 'h519911868_scbox', 'h192331856_scbox', 'h-1482113798_scbox', 'h577349652_scbox');
407 * Can get the ID of the button controlling
408 * a collapseable box by concatenating
409 * this string onto the ID of the box itself.
411 var B_SFIX = "_button";
415 * Returns an element in the current HTML document.
417 * @param elementID Identifier of HTML element
418 * @return HTML element object
420 function getElementObject(elementID) {
422 if (document.getElementById) {
423 elemObj = document.getElementById(elementID);
429 * Closes a collapseable box.
431 * @param boxObj Collapseable box
432 * @param buttonObj Button controlling box
434 function closeBox(boxObj, buttonObj) {
435 if (boxObj == null || buttonObj == null) {
436 // Box or button not found
438 // Change 'display' CSS property of box
439 boxObj.style.display="none";
441 // Change text of button
442 if (boxObj.style.display=="none") {
443 buttonObj.value=" + ";
449 * Opens a collapseable box.
451 * @param boxObj Collapseable box
452 * @param buttonObj Button controlling box
454 function openBox(boxObj, buttonObj) {
455 if (boxObj == null || buttonObj == null) {
456 // Box or button not found
458 // Change 'display' CSS property of box
459 boxObj.style.display="block";
461 // Change text of button
462 if (boxObj.style.display=="block") {
463 buttonObj.value=" - ";
469 * Sets the state of a collapseable box.
471 * @param boxID Identifier of box
472 * @param open If true, box is "opened",
473 * Otherwise, box is "closed".
475 function setState(boxID, open) {
476 var boxObj = getElementObject(boxID);
477 var buttonObj = getElementObject(boxID+B_SFIX);
478 if (boxObj == null || buttonObj == null) {
479 // Box or button not found
481 openBox(boxObj, buttonObj);
482 // Make button visible
483 buttonObj.style.display="inline";
485 closeBox(boxObj, buttonObj);
486 // Make button visible
487 buttonObj.style.display="inline";
492 * Switches the state of a collapseable box, e.g.
493 * if it's opened, it'll be closed, and vice versa.
495 * @param boxID Identifier of box
497 function switchState(boxID) {
498 var boxObj = getElementObject(boxID);
499 var buttonObj = getElementObject(boxID+B_SFIX);
500 if (boxObj == null || buttonObj == null) {
501 // Box or button not found
502 } else if (boxObj.style.display=="none") {
503 // Box is closed, so open it
504 openBox(boxObj, buttonObj);
505 } else if (boxObj.style.display=="block") {
506 // Box is opened, so close it
507 closeBox(boxObj, buttonObj);
512 * Closes all boxes in a given list.
514 * @param boxList Array of box IDs
516 function collapseAll(boxList) {
518 for (idx = 0; idx < boxList.length; idx++) {
519 var boxObj = getElementObject(boxList[idx]);
520 var buttonObj = getElementObject(boxList[idx]+B_SFIX);
521 closeBox(boxObj, buttonObj);
526 * Open all boxes in a given list.
528 * @param boxList Array of box IDs
530 function expandAll(boxList) {
532 for (idx = 0; idx < boxList.length; idx++) {
533 var boxObj = getElementObject(boxList[idx]);
534 var buttonObj = getElementObject(boxList[idx]+B_SFIX);
535 openBox(boxObj, buttonObj);
540 * Makes all the control buttons of boxes appear.
542 * @param boxList Array of box IDs
544 function viewControlButtons(boxList) {
546 for (idx = 0; idx < boxList.length; idx++) {
547 buttonObj = getElementObject(boxList[idx]+B_SFIX);
548 if (buttonObj != null) {
549 buttonObj.style.display = "inline";
555 * Makes all the control buttons of boxes disappear.
557 * @param boxList Array of box IDs
559 function hideControlButtons(boxList) {
561 for (idx = 0; idx < boxList.length; idx++) {
562 buttonObj = getElementObject(boxList[idx]+B_SFIX);
563 if (buttonObj != null) {
564 buttonObj.style.display = "none";
570 * Sets the page for either printing mode
571 * or viewing mode. In printing mode, the page
572 * is made to be more readable when printing it out.
573 * In viewing mode, the page is more browsable.
575 * @param isPrinterVersion If true, display in
576 * printing mode; otherwise,
579 function displayMode(isPrinterVersion) {
581 if (isPrinterVersion) {
582 // Hide global control buttons
583 obj = getElementObject("globalControls");
585 obj.style.visibility = "hidden";
588 obj = getElementObject("legend");
590 obj.style.display = "none";
592 obj = getElementObject("legendTOC");
594 obj.style.display = "none";
597 obj = getElementObject("glossary");
599 obj.style.display = "none";
601 obj = getElementObject("glossaryTOC");
603 obj.style.display = "none";
606 // Expand all diagrams
607 expandAll(diagramBoxes);
608 // Expand all logical diagrams
609 expandAll(logicalDiagramBoxes);
610 // Expand all XML Instance Representation tables
612 // Expand all Schema Component Representation tables
615 // Hide Control buttons
616 hideControlButtons(diagramBoxes);
617 hideControlButtons(logicalDiagramBoxes);
618 hideControlButtons(xiBoxes);
619 hideControlButtons(scBoxes);
621 // View global control buttons
622 obj = getElementObject("globalControls");
624 obj.style.visibility = "visible";
627 obj = getElementObject("legend");
629 obj.style.display = "block";
631 obj = getElementObject("legendTOC");
633 obj.style.display = "block";
636 obj = getElementObject("glossary");
638 obj.style.display = "block";
640 obj = getElementObject("glossaryTOC");
642 obj.style.display = "block";
645 // Expand all diagram boxes
646 expandAll(diagramBoxes);
647 // Collapse all logical diagram boxes.
648 collapseAll(logicalDiagramBoxes);
649 // Expand all XML Instance Representation tables
651 // Collapse all Schema Component Representation tables
652 collapseAll(scBoxes);
654 // View Control buttons
655 viewControlButtons(diagramBoxes);
656 viewControlButtons(logicalDiagramBoxes);
657 viewControlButtons(xiBoxes);
658 viewControlButtons(scBoxes);
666 <script type="text/javascript">
671 * Counter of documentation windows
672 * Used to give each window a unique name
677 * Opens up a window displaying the documentation
678 * of a schema component in the XML Instance
679 * Representation table.
681 * @param compDesc Description of schema component
682 * @param compName Name of schema component
683 * @param docTextArray Array containing the paragraphs
684 * of the new document
686 function viewDocumentation(compDesc, compName, docTextArray) {
692 /* Generate content */
693 var actualText = "<html>";
694 actualText += "<head><title>";
695 actualText += compDesc;
696 if (compName != '') {
697 actualText += ": " + compName;
699 actualText += "</title></head>";
700 actualText += "<body bgcolor=\"#FFFFEE\">";
702 actualText += "<p style=\"font-family: Arial, sans-serif; font-size: 12pt; font-weight: bold; letter-spacing:1px;\">";
703 actualText += compDesc;
704 if (compName != '') {
705 actualText += ": <span style=\"color:#006699\">" + compName + "</span>";
707 actualText += "</p>";
710 for (idx = 0; idx < docTextArray.length; idx++) {
711 actualText += "<p style=\"font-family: Arial, sans-serif; font-size: 10pt;\">" + docTextArray[idx] + "</p>";
713 // Link to close window
714 actualText += "<a href=\"javascript:void(0)\" onclick=\"window.close();\" style=\"font-family: Arial, sans-serif; font-size: 8pt;\">Close</a>";
715 actualText += "</body></html>";
719 var docWindow = window.open("", "documentation"+windowCount, "toolbar=no,location=no,status=no,menubar=no,scrollbars=yes,resizable,alwaysRaised,dependent,titlebar=no,width="+width+",height="+height+",screenX="+locX+",left="+locX+",screenY="+locY+",top="+locY);
720 docWindow.document.write(actualText);
728 <a name="top">Documentation for phyloXML 1.00</a>
730 <div style="float: right;">
731 <div id="printerControls" style="display:none;">
732 <input type="checkbox" onclick="displayMode(this.checked)"/>Printer-friendly Version</div>
733 <script type="text/javascript">
736 var pc = getElementObject("printerControls");
738 pc.style.display="block";
743 <div id="globalControls" style="display:none">
744 <strong>Logical Diagram:</strong>
746 <span style="margin-left: 1em; white-space: nowrap">[ <a href="javascript:void(0)" onclick="expandAll(logicalDiagramBoxes)">Expand All</a> | <a href="javascript:void(0)" onclick="collapseAll(logicalDiagramBoxes)">Collapse All</a> ]</span>
749 <strong>XML Instance Representation:</strong>
751 <span style="margin-left: 1em; white-space: nowrap">[ <a href="javascript:void(0)" onclick="expandAll(xiBoxes)">Expand All</a> | <a href="javascript:void(0)" onclick="collapseAll(xiBoxes)">Collapse All</a> ]</span>
754 <strong>Diagram:</strong>
756 <span style="margin-left: 1em; white-space: nowrap">[ <a href="javascript:void(0)" onclick="expandAll(diagramBoxes)">Expand All</a> | <a href="javascript:void(0)" onclick="collapseAll(diagramBoxes)">Collapse All</a> ]</span>
759 <strong>Schema Component Representation:</strong>
761 <span style="margin-left: 1em; white-space: nowrap">[ <a href="javascript:void(0)" onclick="expandAll(scBoxes)">Expand All</a> | <a href="javascript:void(0)" onclick="collapseAll(scBoxes)">Collapse All</a> ]</span>
763 <script type="text/javascript">
766 var gc = getElementObject("globalControls");
768 gc.style.display="block";
774 <h2>Table of Contents</h2>
777 <a href="#SchemaProperties">Schema Document Properties</a>
780 <a href="#SchemaDeclarations">Global Declarations</a>
783 <a href="#h270234806">Element: <strong>phyloxml</strong>
789 <a href="#SchemaDefinitions">Global Definitions</a>
792 <a href="#h-788356801">Complex Type: <strong>Accession</strong>
796 <a href="#h917087604">Complex Type: <strong>Annotation</strong>
800 <a href="#h1535743041">Complex Type: <strong>BinaryCharacterList</strong>
804 <a href="#h-1514309680">Complex Type: <strong>BinaryCharacters</strong>
808 <a href="#h-1691165380">Complex Type: <strong>BranchColor</strong>
812 <a href="#h-1124608460">Complex Type: <strong>Clade</strong>
816 <a href="#h192331856">Complex Type: <strong>CladeRelation</strong>
820 <a href="#h-993584945">Complex Type: <strong>Confidence</strong>
824 <a href="#h517931443">Complex Type: <strong>Date</strong>
828 <a href="#h-979596407">Complex Type: <strong>Distribution</strong>
832 <a href="#h259010940">Complex Type: <strong>DomainArchitecture</strong>
836 <a href="#h-436501026">Complex Type: <strong>Events</strong>
840 <a href="#h-853091232">Complex Type: <strong>Id</strong>
844 <a href="#h535307528">Complex Type: <strong>Phylogeny</strong>
848 <a href="#h155831896">Complex Type: <strong>Phyloxml</strong>
852 <a href="#h-1112505301">Complex Type: <strong>Point</strong>
856 <a href="#h332351765">Complex Type: <strong>Polygon</strong>
860 <a href="#h158033242">Complex Type: <strong>Property</strong>
864 <a href="#h-1389097534">Complex Type: <strong>ProteinDomain</strong>
868 <a href="#h401516646">Complex Type: <strong>Reference</strong>
872 <a href="#h-1794244794">Complex Type: <strong>Sequence</strong>
876 <a href="#h-802965662">Complex Type: <strong>SequenceRelation</strong>
880 <a href="#h888650454">Complex Type: <strong>Taxonomy</strong>
884 <a href="#h-676012345">Complex Type: <strong>Uri</strong>
888 <a href="#h-763252414">Simple Type: <strong>AppliesTo</strong>
892 <a href="#h-676028775">Simple Type: <strong>Doi</strong>
896 <a href="#h1358103055">Simple Type: <strong>EventType</strong>
900 <a href="#h-213750342">Simple Type: <strong>MolSeq</strong>
904 <a href="#h-54338178">Simple Type: <strong>PropertyDataType</strong>
908 <a href="#h518348337">Simple Type: <strong>Rank</strong>
912 <a href="#h519911868">Simple Type: <strong>SequenceRelationType</strong>
916 <a href="#h935679102">Simple Type: <strong>SequenceSymbol</strong>
920 <a href="#h1408823200">Simple Type: <strong>SequenceType</strong>
924 <a href="#h712147427">Simple Type: <strong>TaxonomyCode</strong>
928 <a href="#h577349652">Simple Type: <strong>id_ref</strong>
932 <a href="#h-1482113798">Simple Type: <strong>id_source</strong>
936 <a href="#h-675984882">Simple Type: <strong>ref</strong>
942 <ul id="legendTOC" style="margin-top: 0em">
944 <a href="#Legend">Legend</a>
947 <ul id="glossaryTOC" style="margin-top: 0em">
949 <a href="#Glossary">Glossary</a>
952 <div style="text-align: right; clear: both;">
953 <a href="#top">top</a>
957 <a name="SchemaProperties">Schema Document Properties</a>
959 <table class="properties">
962 <a title="Look up 'Target Namespace' in glossary"
963 href="phyloxml.xsd.html#term_TargetNS">Target Namespace</a>
966 <span class="targetNS">http://www.phyloxml.org</span>
970 <th>Element and Attribute Namespaces</th>
973 <li>Global element and attribute declarations belong to this schema's target namespace.</li>
974 <li>By default, local element declarations belong to this schema's target namespace.</li>
975 <li>By default, local attribute declarations have no namespace.</li>
980 <th>Documentation</th>
981 <td class="documentation"> phyloXML is an XML language to describe phylogenies and associated data. Version: 1.00.
982 License: LGPL. Copyright (c) 2008-2009 Christian M Zmasek.</td>
985 <h3>Declared Namespaces</h3>
986 <table class="namespaces">
993 <a name="ns_xml">xml</a>
995 <td>http://www.w3.org/XML/1998/namespace</td>
999 <a name="ns_phy">phy</a>
1002 <span class="targetNS">http://www.phyloxml.org</span>
1007 <a name="ns_xs">xs</a>
1009 <td>http://www.w3.org/2001/XMLSchema</td>
1012 <div class="schemaComponent box">
1014 <input type="button" id="schema_scbox_button" class="control"
1015 onclick="switchState('schema_scbox'); return false;"
1016 style="display: none"/>
1017 <span class="caption">Schema Component Representation</span>
1019 <div id="schema_scbox" class="contents">
1020 <div style="margin-left: 0em"><<span class="scTag">xs:schema</span>
1021 <span class="scTag">targetNamespace</span>="<span class="scContent">http://www.phyloxml.org</span>" <span class="scTag">elementFormDefault</span>="<span class="scContent">qualified</span>" <span class="scTag">attributeFormDefault</span>="<span class="scContent">unqualified</span>"><div class="scContent" style="margin-left: 1.5em">...</div></<span class="scTag">xs:schema</span>></div>
1023 <script type="text/javascript">
1025 setState('schema_scbox', false);
1029 <div style="text-align: right; clear: both;">
1030 <a href="#top">top</a>
1034 <a name="SchemaDeclarations">Global Declarations</a>
1036 <h3>Element: <a name="h270234806" class="name">phyloxml</a>
1038 <table class="properties">
1047 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Phyloxml" type definition." href="#h155831896">Phyloxml</a>
1053 <a title="Look up 'Nillable' in glossary" href="phyloxml.xsd.html#term_Nillable">Nillable</a>
1059 <a title="Look up 'Abstract' in glossary" href="phyloxml.xsd.html#term_Abstract">Abstract</a>
1064 <div class="sample box">
1066 <input type="button" id="h270234806_logicalDiagram_button" class="control"
1067 onclick="switchState('h270234806_logicalDiagram'); return false;"
1068 style="display: none"/>
1069 <span class="caption">Logical Diagram</span>
1071 <div id="h270234806_logicalDiagram" class="contents">
1072 <img usemap="#h1900732667" src="schemaDiagrams/h1900732667.png"/>
1074 Map ref: file:/D:/WORK/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester-atv/resources/phyloxml_schema/1.00//schemaDiagrams/h1900732667.map--><map name="h1900732667">
1077 <script type="text/javascript">
1079 setState('h270234806_logicalDiagram', false);
1083 <div class="sample box">
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1087 style="display: none"/>
1088 <span class="caption">XML Instance Representation</span>
1090 <div id="h270234806_xibox" class="contents">
1091 <div style="margin-left: 0em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:phyloxml> <br/>
1092 <span class="group" style="margin-left: 1.5em">Start <a title="Look up 'Sequence' in glossary" href="phyloxml.xsd.html#term_Sequence">Sequence</a>
1093 <span class="occurs">[1..*]</span>
1096 <div style="margin-left: 3em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:phylogeny> <span class="type">
1097 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Phylogeny" type definition." href="#h535307528">Phylogeny</a>
1098 </span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:phylogeny> <span class="occurs">[0..*]</span>
1100 <div class="other" style="margin-left: 3em">Allow any elements from a namespace other than this schema's namespace (lax validation). <span class="occurs">[0..*]</span>
1102 <span class="group" style="margin-left: 1.5em">End Sequence</span>
1103 <br/></<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:phyloxml></div>
1105 <script type="text/javascript">
1107 setState('h270234806_xibox', true);
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1114 onclick="switchState('h270234806_diagram'); return false;"
1115 style="display: none"/>
1116 <span class="caption">Diagram</span>
1118 <div id="h270234806_diagram" class="contents">
1119 <img usemap="#h482833585" src="schemaDiagrams/h482833585.png"/>
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1136 onclick="switchState('h270234806_scbox'); return false;"
1137 style="display: none"/>
1138 <span class="caption">Schema Component Representation</span>
1140 <div id="h270234806_scbox" class="contents">
1141 <div style="margin-left: 0em"><<span class="scTag">xs:element</span>
1142 <span class="scTag">name</span>="<span class="scContent">phyloxml</span>" <span class="scTag">type</span>="<span class="scContent">
1144 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Phyloxml" type definition." href="#h155831896">Phyloxml</a>
1148 <script type="text/javascript">
1150 setState('h270234806_scbox', false);
1154 <div style="text-align: right; clear: both;">
1155 <a href="#top">top</a>
1159 <a name="SchemaDefinitions">Global Definitions</a>
1161 <h3>Complex Type: <a name="h-788356801" class="name">Accession</a>
1163 <table class="hierarchy">
1165 <th>Super-types:</th>
1168 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span> < <strong>Accession</strong> (by extension)</td>
1175 <table class="properties">
1181 <th>Used by (from the same schema document)</th>
1182 <td>Complex Type <b>
1183 <a href="#h-1794244794">Sequence</a>
1189 <a title="Look up 'Abstract' in glossary" href="phyloxml.xsd.html#term_Abstract">Abstract</a>
1194 <th>Documentation</th>
1195 <td class="documentation"> Element Accession is used to capture the local part in a sequence identifier (e.g. 'P17304'
1196 in 'UniProtKB:P17304', in which case the 'source' attribute would be 'UniProtKB'). </td>
1199 <div class="sample box">
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1202 onclick="switchState('h-788356801_xibox'); return false;"
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1204 <span class="caption">XML Instance Representation</span>
1206 <div id="h-788356801_xibox" class="contents">
1207 <div style="margin-left: 0em"><...<br/>
1208 <span style="margin-left: 0.5em" class="newFields"> source="<span class="type">
1209 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
1210 <span class="occurs">[1]</span>"</span>> <br/>
1211 <span style="margin-left: 1.5em">
1213 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
1215 <br/></...></div>
1217 <script type="text/javascript">
1219 setState('h-788356801_xibox', true);
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1226 onclick="switchState('h-788356801_diagram'); return false;"
1227 style="display: none"/>
1228 <span class="caption">Diagram</span>
1230 <div id="h-788356801_diagram" class="contents">
1231 <img usemap="#h-1142642744" src="schemaDiagrams/h-1142642744.png"/>
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1245 onclick="switchState('h-788356801_scbox'); return false;"
1246 style="display: none"/>
1247 <span class="caption">Schema Component Representation</span>
1249 <div id="h-788356801_scbox" class="contents">
1250 <div style="margin-left: 0em"><<span class="scTag">xs:complexType</span>
1251 <span class="scTag">name</span>="<span class="scContent">Accession</span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:simpleContent</span>><div style="margin-left: 1.5em"><<span class="scTag">xs:extension</span>
1252 <span class="scTag">base</span>="<span class="scContent">
1254 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
1255 </span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:attribute</span>
1256 <span class="scTag">name</span>="<span class="scContent">source</span>" <span class="scTag">type</span>="<span class="scContent">
1258 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
1259 </span>" <span class="scTag">use</span>="<span class="scContent">required</span>"/></div></<span class="scTag">xs:extension</span>></div></<span class="scTag">xs:simpleContent</span>></div></<span class="scTag">xs:complexType</span>></div>
1261 <script type="text/javascript">
1263 setState('h-788356801_scbox', false);
1267 <div style="text-align: right; clear: both;">
1268 <a href="#top">top</a>
1271 <h3>Complex Type: <a name="h917087604" class="name">Annotation</a>
1273 <table class="hierarchy">
1275 <th>Super-types:</th>
1283 <table class="properties">
1289 <th>Used by (from the same schema document)</th>
1290 <td>Complex Type <b>
1291 <a href="#h-1794244794">Sequence</a>
1297 <a title="Look up 'Abstract' in glossary" href="phyloxml.xsd.html#term_Abstract">Abstract</a>
1302 <th>Documentation</th>
1303 <td class="documentation"> The annotation of a molecular sequence. It is recommended to annotate by using the optional
1304 'ref' attribute (some examples of acceptable values for the ref attribute: 'GO:0008270',
1305 'KEGG:Tetrachloroethene degradation', 'EC:1.1.1.1'). Optional element 'desc' allows for a free text
1306 description. Optional element 'confidence' is used to state the type and value of support for a annotation.
1307 Similarly, optional attribute 'evidence' is used to describe the evidence for a annotation as free text
1308 (e.g. 'experimental'). Optional element 'property' allows for further, typed and referenced annotations from
1309 external resources.</td>
1312 <div class="sample box">
1314 <input type="button" id="h917087604_xibox_button" class="control"
1315 onclick="switchState('h917087604_xibox'); return false;"
1316 style="display: none"/>
1317 <span class="caption">XML Instance Representation</span>
1319 <div id="h917087604_xibox" class="contents">
1320 <div style="margin-left: 0em"><...<br/>
1321 <span style="margin-left: 0.5em"> ref="<span class="type">
1322 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "ref" type definition." href="#h-675984882">ref</a>
1324 <span class="occurs">[0..1]</span>"</span>
1326 <span style="margin-left: 0.5em"> source="<span class="type">
1327 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
1328 <span class="occurs">[0..1]</span>"</span>
1330 <span style="margin-left: 0.5em"> evidence="<span class="type">
1331 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
1332 <span class="occurs">[0..1]</span>"</span>
1334 <span style="margin-left: 0.5em"> type="<span class="type">
1335 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
1336 <span class="occurs">[0..1]</span>"</span>> <br/>
1337 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:desc> <span class="type">
1338 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:desc> <span class="occurs">[0..1]</span>
1340 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:confidence> <span class="type">
1341 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Confidence" type definition." href="#h-993584945">Confidence</a>
1342 </span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:confidence> <span class="occurs">[0..1]</span>
1344 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:property> <span class="type">
1345 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Property" type definition." href="#h158033242">Property</a>
1346 </span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:property> <span class="occurs">[0..*]</span>
1348 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:uri> <span class="type">
1349 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Uri" type definition." href="#h-676012345">Uri</a>
1350 </span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:uri> <span class="occurs">[0..1]</span>
1351 </div></...></div>
1353 <script type="text/javascript">
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1359 <div class="sample box">
1361 <input type="button" id="h917087604_diagram_button" class="control"
1362 onclick="switchState('h917087604_diagram'); return false;"
1363 style="display: none"/>
1364 <span class="caption">Diagram</span>
1366 <div id="h917087604_diagram" class="contents">
1367 <img usemap="#h624412339" src="schemaDiagrams/h624412339.png"/>
1369 Map ref: file:/D:/WORK/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester-atv/resources/phyloxml_schema/1.00//schemaDiagrams/h624412339.map--><map name="h624412339">
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1394 style="display: none"/>
1395 <span class="caption">Schema Component Representation</span>
1397 <div id="h917087604_scbox" class="contents">
1398 <div style="margin-left: 0em"><<span class="scTag">xs:complexType</span>
1399 <span class="scTag">name</span>="<span class="scContent">Annotation</span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:sequence</span>><div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
1400 <span class="scTag">name</span>="<span class="scContent">desc</span>" <span class="scTag">type</span>="<span class="scContent">
1402 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
1403 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>"/></div>
1404 <div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
1405 <span class="scTag">name</span>="<span class="scContent">confidence</span>" <span class="scTag">type</span>="<span class="scContent">
1407 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Confidence" type definition." href="#h-993584945">Confidence</a>
1409 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>"/></div>
1410 <div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
1411 <span class="scTag">name</span>="<span class="scContent">property</span>" <span class="scTag">type</span>="<span class="scContent">
1413 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Property" type definition." href="#h158033242">Property</a>
1415 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>" <span class="scTag">maxOccurs</span>="<span class="scContent">unbounded</span>"/></div>
1416 <div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
1417 <span class="scTag">name</span>="<span class="scContent">uri</span>" <span class="scTag">type</span>="<span class="scContent">
1419 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Uri" type definition." href="#h-676012345">Uri</a>
1421 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>"/></div></<span class="scTag">xs:sequence</span>></div>
1422 <div style="margin-left: 1.5em"><<span class="scTag">xs:attribute</span>
1423 <span class="scTag">name</span>="<span class="scContent">ref</span>" <span class="scTag">type</span>="<span class="scContent">
1425 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "ref" type definition." href="#h-675984882">ref</a>
1428 <div style="margin-left: 1.5em"><<span class="scTag">xs:attribute</span>
1429 <span class="scTag">name</span>="<span class="scContent">source</span>" <span class="scTag">type</span>="<span class="scContent">
1431 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
1433 <div style="margin-left: 1.5em"><<span class="scTag">xs:attribute</span>
1434 <span class="scTag">name</span>="<span class="scContent">evidence</span>" <span class="scTag">type</span>="<span class="scContent">
1436 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
1438 <div style="margin-left: 1.5em"><<span class="scTag">xs:attribute</span>
1439 <span class="scTag">name</span>="<span class="scContent">type</span>" <span class="scTag">type</span>="<span class="scContent">
1441 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
1442 </span>"/></div></<span class="scTag">xs:complexType</span>></div>
1444 <script type="text/javascript">
1446 setState('h917087604_scbox', false);
1450 <div style="text-align: right; clear: both;">
1451 <a href="#top">top</a>
1454 <h3>Complex Type: <a name="h1535743041" class="name">BinaryCharacterList</a>
1456 <table class="hierarchy">
1458 <th>Super-types:</th>
1466 <table class="properties">
1469 <td>BinaryCharacterList</td>
1472 <th>Used by (from the same schema document)</th>
1473 <td>Complex Type <b>
1474 <a href="#h-1514309680">BinaryCharacters</a>
1475 </b>, Complex Type <b>
1476 <a href="#h-1514309680">BinaryCharacters</a>
1477 </b>, Complex Type <b>
1478 <a href="#h-1514309680">BinaryCharacters</a>
1479 </b>, Complex Type <b>
1480 <a href="#h-1514309680">BinaryCharacters</a>
1486 <a title="Look up 'Abstract' in glossary" href="phyloxml.xsd.html#term_Abstract">Abstract</a>
1491 <div class="sample box">
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1496 <span class="caption">XML Instance Representation</span>
1498 <div id="h1535743041_xibox" class="contents">
1499 <div style="margin-left: 0em"><...> <br/>
1500 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:bc> <span class="type">
1501 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:bc> <span class="occurs">[1..*]</span>
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1514 style="display: none"/>
1515 <span class="caption">Diagram</span>
1517 <div id="h1535743041_diagram" class="contents">
1518 <img usemap="#h508496390" src="schemaDiagrams/h508496390.png"/>
1520 Map ref: file:/D:/WORK/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester-atv/resources/phyloxml_schema/1.00//schemaDiagrams/h508496390.map--><map name="h508496390">
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1532 onclick="switchState('h1535743041_scbox'); return false;"
1533 style="display: none"/>
1534 <span class="caption">Schema Component Representation</span>
1536 <div id="h1535743041_scbox" class="contents">
1537 <div style="margin-left: 0em"><<span class="scTag">xs:complexType</span>
1538 <span class="scTag">name</span>="<span class="scContent">BinaryCharacterList</span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:sequence</span>><div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
1539 <span class="scTag">name</span>="<span class="scContent">bc</span>" <span class="scTag">type</span>="<span class="scContent">
1541 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
1542 </span>" <span class="scTag">maxOccurs</span>="<span class="scContent">unbounded</span>"/></div></<span class="scTag">xs:sequence</span>></div></<span class="scTag">xs:complexType</span>></div>
1544 <script type="text/javascript">
1546 setState('h1535743041_scbox', false);
1550 <div style="text-align: right; clear: both;">
1551 <a href="#top">top</a>
1554 <h3>Complex Type: <a name="h-1514309680" class="name">BinaryCharacters</a>
1556 <table class="hierarchy">
1558 <th>Super-types:</th>
1566 <table class="properties">
1569 <td>BinaryCharacters</td>
1572 <th>Used by (from the same schema document)</th>
1573 <td>Complex Type <b>
1574 <a href="#h-1124608460">Clade</a>
1580 <a title="Look up 'Abstract' in glossary" href="phyloxml.xsd.html#term_Abstract">Abstract</a>
1585 <th>Documentation</th>
1586 <td class="documentation"> The names and/or counts of binary characters present, gained, and lost at the root of a
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1595 <span class="caption">XML Instance Representation</span>
1597 <div id="h-1514309680_xibox" class="contents">
1598 <div style="margin-left: 0em"><...<br/>
1599 <span style="margin-left: 0.5em"> type="<span class="type">
1600 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
1601 <span class="occurs">[0..1]</span>"</span>
1603 <span style="margin-left: 0.5em"> gained_count="<span class="type">
1604 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:nonNegativeInteger</span>
1605 <span class="occurs">[0..1]</span>"</span>
1607 <span style="margin-left: 0.5em"> lost_count="<span class="type">
1608 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:nonNegativeInteger</span>
1609 <span class="occurs">[0..1]</span>"</span>
1611 <span style="margin-left: 0.5em"> present_count="<span class="type">
1612 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:nonNegativeInteger</span>
1613 <span class="occurs">[0..1]</span>"</span>
1615 <span style="margin-left: 0.5em"> absent_count="<span class="type">
1616 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:nonNegativeInteger</span>
1617 <span class="occurs">[0..1]</span>"</span>> <br/>
1618 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:gained> <span class="type">
1619 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "BinaryCharacterList" type definition." href="#h1535743041">BinaryCharacterList</a>
1620 </span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:gained> <span class="occurs">[0..1]</span>
1622 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:lost> <span class="type">
1623 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "BinaryCharacterList" type definition." href="#h1535743041">BinaryCharacterList</a>
1624 </span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:lost> <span class="occurs">[0..1]</span>
1626 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:present> <span class="type">
1627 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "BinaryCharacterList" type definition." href="#h1535743041">BinaryCharacterList</a>
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1648 <div id="h-1514309680_diagram" class="contents">
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1677 <span class="caption">Schema Component Representation</span>
1679 <div id="h-1514309680_scbox" class="contents">
1680 <div style="margin-left: 0em"><<span class="scTag">xs:complexType</span>
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1741 <h3>Complex Type: <a name="h-1691165380" class="name">BranchColor</a>
1743 <table class="hierarchy">
1745 <th>Super-types:</th>
1753 <table class="properties">
1756 <td>BranchColor</td>
1759 <th>Used by (from the same schema document)</th>
1760 <td>Complex Type <b>
1761 <a href="#h-1124608460">Clade</a>
1767 <a title="Look up 'Abstract' in glossary" href="phyloxml.xsd.html#term_Abstract">Abstract</a>
1772 <th>Documentation</th>
1773 <td class="documentation"> This indicates the color of a clade when rendered (the color applies to the whole clade
1774 unless overwritten by the color(s) of sub clades).</td>
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1853 <a href="#top">top</a>
1856 <h3>Complex Type: <a name="h-1124608460" class="name">Clade</a>
1858 <table class="hierarchy">
1860 <th>Super-types:</th>
1868 <table class="properties">
1874 <th>Used by (from the same schema document)</th>
1875 <td>Complex Type <b>
1876 <a href="#h535307528">Phylogeny</a>
1877 </b>, Complex Type <b>
1878 <a href="#h-1124608460">Clade</a>
1884 <a title="Look up 'Abstract' in glossary" href="phyloxml.xsd.html#term_Abstract">Abstract</a>
1889 <th>Documentation</th>
1890 <td class="documentation"> Element Clade is used in a recursive manner to describe the topology of a phylogenetic tree.
1891 The parent branch length of a clade can be described either with the 'branch_length' element or the
1892 'branch_length' attribute (it is not recommended to use both at the same time, though). Usage of the
1893 'branch_length' attribute allows for a less verbose description. Element 'confidence' is used to indicate
1894 the support for a clade/parent branch. Element 'events' is used to describe such events as gene-duplications
1895 at the root node/parent branch of a clade. Element 'width' is the branch width for this clade (including
1896 parent branch). Both 'color' and 'width' elements apply for the whole clade unless overwritten in-sub
1897 clades. Attribute 'id_source' is used to link other elements to a clade (on the xml-level).
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1932 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "BranchColor" type definition." href="#h-1691165380">BranchColor</a>
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1935 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:node_id> <span class="type">
1936 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Id" type definition." href="#h-853091232">Id</a>
1937 </span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:node_id> <span class="occurs">[0..1]</span>
1939 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:taxonomy> <span class="type">
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1941 </span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:taxonomy> <span class="occurs">[0..*]</span>
1943 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:sequence> <span class="type">
1944 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Sequence" type definition." href="#h-1794244794">Sequence</a>
1945 </span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:sequence> <span class="occurs">[0..*]</span>
1947 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:events> <span class="type">
1948 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Events" type definition." href="#h-436501026">Events</a>
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1951 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:binary_characters> <span class="type">
1952 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "BinaryCharacters" type definition." href="#h-1514309680">BinaryCharacters</a>
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1955 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:distribution> <span class="type">
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1961 </span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:date> <span class="occurs">[0..1]</span>
1963 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:reference> <span class="type">
1964 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Reference" type definition." href="#h401516646">Reference</a>
1965 </span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:reference> <span class="occurs">[0..*]</span>
1967 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:property> <span class="type">
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1969 </span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:property> <span class="occurs">[0..*]</span>
1971 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:clade> <span class="type">
1972 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Clade" type definition." href="#h-1124608460">Clade</a>
1973 </span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:clade> <span class="occurs">[0..*]</span>
1975 <div class="other" style="margin-left: 1.5em">Allow any elements from a namespace other than this schema's namespace (lax validation). <span class="occurs">[0..*]</span>
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2047 <div style="margin-left: 0em"><<span class="scTag">xs:complexType</span>
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2053 <div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
2054 <span class="scTag">name</span>="<span class="scContent">branch_length</span>" <span class="scTag">type</span>="<span class="scContent">
2056 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:double</span>
2057 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>"/></div>
2058 <div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
2059 <span class="scTag">name</span>="<span class="scContent">confidence</span>" <span class="scTag">type</span>="<span class="scContent">
2061 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Confidence" type definition." href="#h-993584945">Confidence</a>
2063 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>" <span class="scTag">maxOccurs</span>="<span class="scContent">unbounded</span>"/></div>
2064 <div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
2065 <span class="scTag">name</span>="<span class="scContent">width</span>" <span class="scTag">type</span>="<span class="scContent">
2067 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:double</span>
2068 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>"/></div>
2069 <div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
2070 <span class="scTag">name</span>="<span class="scContent">color</span>" <span class="scTag">type</span>="<span class="scContent">
2072 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "BranchColor" type definition." href="#h-1691165380">BranchColor</a>
2074 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>"/></div>
2075 <div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
2076 <span class="scTag">name</span>="<span class="scContent">node_id</span>" <span class="scTag">type</span>="<span class="scContent">
2078 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Id" type definition." href="#h-853091232">Id</a>
2080 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>"/></div>
2081 <div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
2082 <span class="scTag">name</span>="<span class="scContent">taxonomy</span>" <span class="scTag">type</span>="<span class="scContent">
2084 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Taxonomy" type definition." href="#h888650454">Taxonomy</a>
2086 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>" <span class="scTag">maxOccurs</span>="<span class="scContent">unbounded</span>"/></div>
2087 <div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
2088 <span class="scTag">name</span>="<span class="scContent">sequence</span>" <span class="scTag">type</span>="<span class="scContent">
2090 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Sequence" type definition." href="#h-1794244794">Sequence</a>
2092 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>" <span class="scTag">maxOccurs</span>="<span class="scContent">unbounded</span>"/></div>
2093 <div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
2094 <span class="scTag">name</span>="<span class="scContent">events</span>" <span class="scTag">type</span>="<span class="scContent">
2096 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Events" type definition." href="#h-436501026">Events</a>
2098 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>"/></div>
2099 <div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
2100 <span class="scTag">name</span>="<span class="scContent">binary_characters</span>" <span class="scTag">type</span>="<span class="scContent">
2102 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "BinaryCharacters" type definition." href="#h-1514309680">BinaryCharacters</a>
2104 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>"/></div>
2105 <div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
2106 <span class="scTag">name</span>="<span class="scContent">distribution</span>" <span class="scTag">type</span>="<span class="scContent">
2108 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Distribution" type definition." href="#h-979596407">Distribution</a>
2110 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>" <span class="scTag">maxOccurs</span>="<span class="scContent">unbounded</span>"/></div>
2111 <div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
2112 <span class="scTag">name</span>="<span class="scContent">date</span>" <span class="scTag">type</span>="<span class="scContent">
2114 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Date" type definition." href="#h517931443">Date</a>
2116 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>"/></div>
2117 <div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
2118 <span class="scTag">name</span>="<span class="scContent">reference</span>" <span class="scTag">type</span>="<span class="scContent">
2120 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Reference" type definition." href="#h401516646">Reference</a>
2122 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>" <span class="scTag">maxOccurs</span>="<span class="scContent">unbounded</span>"/></div>
2123 <div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
2124 <span class="scTag">name</span>="<span class="scContent">property</span>" <span class="scTag">type</span>="<span class="scContent">
2126 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Property" type definition." href="#h158033242">Property</a>
2128 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>" <span class="scTag">maxOccurs</span>="<span class="scContent">unbounded</span>"/></div>
2129 <div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
2130 <span class="scTag">name</span>="<span class="scContent">clade</span>" <span class="scTag">type</span>="<span class="scContent">
2132 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Clade" type definition." href="#h-1124608460">Clade</a>
2134 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>" <span class="scTag">maxOccurs</span>="<span class="scContent">unbounded</span>"/></div>
2135 <div style="margin-left: 1.5em"><<span class="scTag">xs:any</span>
2136 <span class="scTag">minOccurs</span>="<span class="scContent">0</span>" <span class="scTag">maxOccurs</span>="<span class="scContent">unbounded</span>" <span class="scTag">processContents</span>="<span class="scContent">lax</span>" <span class="scTag">namespace</span>="<span class="scContent">##other</span>"/></div></<span class="scTag">xs:sequence</span>></div>
2137 <div style="margin-left: 1.5em"><<span class="scTag">xs:attribute</span>
2138 <span class="scTag">name</span>="<span class="scContent">branch_length</span>" <span class="scTag">type</span>="<span class="scContent">
2140 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:double</span>
2142 <div style="margin-left: 1.5em"><<span class="scTag">xs:attribute</span>
2143 <span class="scTag">name</span>="<span class="scContent">id_source</span>" <span class="scTag">type</span>="<span class="scContent">
2145 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "id_source" type definition." href="#h-1482113798">id_source</a>
2147 </span>"/></div></<span class="scTag">xs:complexType</span>></div>
2149 <script type="text/javascript">
2151 setState('h-1124608460_scbox', false);
2155 <div style="text-align: right; clear: both;">
2156 <a href="#top">top</a>
2159 <h3>Complex Type: <a name="h192331856" class="name">CladeRelation</a>
2161 <table class="hierarchy">
2163 <th>Super-types:</th>
2171 <table class="properties">
2174 <td>CladeRelation</td>
2177 <th>Used by (from the same schema document)</th>
2178 <td>Complex Type <b>
2179 <a href="#h535307528">Phylogeny</a>
2185 <a title="Look up 'Abstract' in glossary" href="phyloxml.xsd.html#term_Abstract">Abstract</a>
2190 <th>Documentation</th>
2191 <td class="documentation"> This is used to express a typed relationship between two clades. For example it could be
2192 used to describe multiple parents of a clade.</td>
2195 <div class="sample box">
2197 <input type="button" id="h192331856_xibox_button" class="control"
2198 onclick="switchState('h192331856_xibox'); return false;"
2199 style="display: none"/>
2200 <span class="caption">XML Instance Representation</span>
2202 <div id="h192331856_xibox" class="contents">
2203 <div style="margin-left: 0em"><...<br/>
2204 <span style="margin-left: 0.5em"> id_ref_0="<span class="type">
2205 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "id_ref" type definition." href="#h577349652">id_ref</a>
2207 <span class="occurs">[1]</span>"</span>
2209 <span style="margin-left: 0.5em"> id_ref_1="<span class="type">
2210 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "id_ref" type definition." href="#h577349652">id_ref</a>
2212 <span class="occurs">[1]</span>"</span>
2214 <span style="margin-left: 0.5em"> distance="<span class="type">
2215 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:double</span>
2216 <span class="occurs">[0..1]</span>"</span>
2218 <span style="margin-left: 0.5em"> type="<span class="type">
2219 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
2220 <span class="occurs">[1]</span>"</span>> <br/>
2221 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:confidence> <span class="type">
2222 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Confidence" type definition." href="#h-993584945">Confidence</a>
2223 </span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:confidence> <span class="occurs">[0..1]</span>
2224 </div></...></div>
2226 <script type="text/javascript">
2228 setState('h192331856_xibox', true);
2232 <div class="sample box">
2234 <input type="button" id="h192331856_diagram_button" class="control"
2235 onclick="switchState('h192331856_diagram'); return false;"
2236 style="display: none"/>
2237 <span class="caption">Diagram</span>
2239 <div id="h192331856_diagram" class="contents">
2240 <img usemap="#h1919634775" src="schemaDiagrams/h1919634775.png"/>
2242 Map ref: file:/D:/WORK/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester-atv/resources/phyloxml_schema/1.00//schemaDiagrams/h1919634775.map--><map name="h1919634775">
2243 <area shape="rect" alt="h-993584945" coords="257,0,383,40"
2244 href="phyloxml.xsd.html#h-993584945"/>
2246 <area shape="rect" alt="h577349652" coords="171,50,301,76"
2247 href="phyloxml.xsd.html#h577349652"/>
2249 <area shape="rect" alt="h577349652" coords="171,86,301,112"
2250 href="phyloxml.xsd.html#h577349652"/>
2254 <script type="text/javascript">
2256 setState('h192331856_diagram', true);
2260 <div class="schemaComponent box">
2262 <input type="button" id="h192331856_scbox_button" class="control"
2263 onclick="switchState('h192331856_scbox'); return false;"
2264 style="display: none"/>
2265 <span class="caption">Schema Component Representation</span>
2267 <div id="h192331856_scbox" class="contents">
2268 <div style="margin-left: 0em"><<span class="scTag">xs:complexType</span>
2269 <span class="scTag">name</span>="<span class="scContent">CladeRelation</span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:sequence</span>><div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
2270 <span class="scTag">name</span>="<span class="scContent">confidence</span>" <span class="scTag">type</span>="<span class="scContent">
2272 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Confidence" type definition." href="#h-993584945">Confidence</a>
2274 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>"/></div></<span class="scTag">xs:sequence</span>></div>
2275 <div style="margin-left: 1.5em"><<span class="scTag">xs:attribute</span>
2276 <span class="scTag">name</span>="<span class="scContent">id_ref_0</span>" <span class="scTag">type</span>="<span class="scContent">
2278 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "id_ref" type definition." href="#h577349652">id_ref</a>
2280 </span>" <span class="scTag">use</span>="<span class="scContent">required</span>"/></div>
2281 <div style="margin-left: 1.5em"><<span class="scTag">xs:attribute</span>
2282 <span class="scTag">name</span>="<span class="scContent">id_ref_1</span>" <span class="scTag">type</span>="<span class="scContent">
2284 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "id_ref" type definition." href="#h577349652">id_ref</a>
2286 </span>" <span class="scTag">use</span>="<span class="scContent">required</span>"/></div>
2287 <div style="margin-left: 1.5em"><<span class="scTag">xs:attribute</span>
2288 <span class="scTag">name</span>="<span class="scContent">distance</span>" <span class="scTag">type</span>="<span class="scContent">
2290 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:double</span>
2292 <div style="margin-left: 1.5em"><<span class="scTag">xs:attribute</span>
2293 <span class="scTag">name</span>="<span class="scContent">type</span>" <span class="scTag">type</span>="<span class="scContent">
2295 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
2296 </span>" <span class="scTag">use</span>="<span class="scContent">required</span>"/></div></<span class="scTag">xs:complexType</span>></div>
2298 <script type="text/javascript">
2300 setState('h192331856_scbox', false);
2304 <div style="text-align: right; clear: both;">
2305 <a href="#top">top</a>
2308 <h3>Complex Type: <a name="h-993584945" class="name">Confidence</a>
2310 <table class="hierarchy">
2312 <th>Super-types:</th>
2315 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:double</span> < <strong>Confidence</strong> (by extension)</td>
2322 <table class="properties">
2328 <th>Used by (from the same schema document)</th>
2329 <td>Complex Type <b>
2330 <a href="#h535307528">Phylogeny</a>
2331 </b>, Complex Type <b>
2332 <a href="#h-1124608460">Clade</a>
2333 </b>, Complex Type <b>
2334 <a href="#h-436501026">Events</a>
2335 </b>, Complex Type <b>
2336 <a href="#h917087604">Annotation</a>
2337 </b>, Complex Type <b>
2338 <a href="#h-802965662">SequenceRelation</a>
2339 </b>, Complex Type <b>
2340 <a href="#h192331856">CladeRelation</a>
2346 <a title="Look up 'Abstract' in glossary" href="phyloxml.xsd.html#term_Abstract">Abstract</a>
2351 <th>Documentation</th>
2352 <td class="documentation"> A general purpose confidence element. For example this can be used to express the bootstrap
2353 support value of a clade (in which case the 'type' attribute is 'bootstrap').</td>
2356 <div class="sample box">
2358 <input type="button" id="h-993584945_xibox_button" class="control"
2359 onclick="switchState('h-993584945_xibox'); return false;"
2360 style="display: none"/>
2361 <span class="caption">XML Instance Representation</span>
2363 <div id="h-993584945_xibox" class="contents">
2364 <div style="margin-left: 0em"><...<br/>
2365 <span style="margin-left: 0.5em" class="newFields"> type="<span class="type">
2366 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
2367 <span class="occurs">[1]</span>"</span>> <br/>
2368 <span style="margin-left: 1.5em">
2370 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:double</span>
2372 <br/></...></div>
2374 <script type="text/javascript">
2376 setState('h-993584945_xibox', true);
2380 <div class="sample box">
2382 <input type="button" id="h-993584945_diagram_button" class="control"
2383 onclick="switchState('h-993584945_diagram'); return false;"
2384 style="display: none"/>
2385 <span class="caption">Diagram</span>
2387 <div id="h-993584945_diagram" class="contents">
2388 <img usemap="#h1603897912" src="schemaDiagrams/h1603897912.png"/>
2390 Map ref: file:/D:/WORK/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester-atv/resources/phyloxml_schema/1.00//schemaDiagrams/h1603897912.map--><map name="h1603897912">
2393 <script type="text/javascript">
2395 setState('h-993584945_diagram', true);
2399 <div class="schemaComponent box">
2401 <input type="button" id="h-993584945_scbox_button" class="control"
2402 onclick="switchState('h-993584945_scbox'); return false;"
2403 style="display: none"/>
2404 <span class="caption">Schema Component Representation</span>
2406 <div id="h-993584945_scbox" class="contents">
2407 <div style="margin-left: 0em"><<span class="scTag">xs:complexType</span>
2408 <span class="scTag">name</span>="<span class="scContent">Confidence</span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:simpleContent</span>><div style="margin-left: 1.5em"><<span class="scTag">xs:extension</span>
2409 <span class="scTag">base</span>="<span class="scContent">
2411 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:double</span>
2412 </span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:attribute</span>
2413 <span class="scTag">name</span>="<span class="scContent">type</span>" <span class="scTag">type</span>="<span class="scContent">
2415 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
2416 </span>" <span class="scTag">use</span>="<span class="scContent">required</span>"/></div></<span class="scTag">xs:extension</span>></div></<span class="scTag">xs:simpleContent</span>></div></<span class="scTag">xs:complexType</span>></div>
2418 <script type="text/javascript">
2420 setState('h-993584945_scbox', false);
2424 <div style="text-align: right; clear: both;">
2425 <a href="#top">top</a>
2428 <h3>Complex Type: <a name="h517931443" class="name">Date</a>
2430 <table class="hierarchy">
2432 <th>Super-types:</th>
2440 <table class="properties">
2446 <th>Used by (from the same schema document)</th>
2447 <td>Complex Type <b>
2448 <a href="#h-1124608460">Clade</a>
2454 <a title="Look up 'Abstract' in glossary" href="phyloxml.xsd.html#term_Abstract">Abstract</a>
2459 <th>Documentation</th>
2460 <td class="documentation"> A date associated with a clade/node. Its value can be numerical by using the 'value' element
2461 and/or free text with the 'desc' element' (e.g. 'Silurian'). If a numerical value is used, it is recommended
2462 to employ the 'unit' attribute to indicate the type of the numerical value (e.g. 'mya' for 'million years
2466 <div class="sample box">
2468 <input type="button" id="h517931443_xibox_button" class="control"
2469 onclick="switchState('h517931443_xibox'); return false;"
2470 style="display: none"/>
2471 <span class="caption">XML Instance Representation</span>
2473 <div id="h517931443_xibox" class="contents">
2474 <div style="margin-left: 0em"><...<br/>
2475 <span style="margin-left: 0.5em"> unit="<span class="type">
2476 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
2477 <span class="occurs">[0..1]</span>"</span>
2479 <span style="margin-left: 0.5em"> range="<span class="type">
2480 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:decimal</span>
2481 <span class="occurs">[0..1]</span>"</span>> <br/>
2482 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:desc> <span class="type">
2483 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:desc> <span class="occurs">[0..1]</span>
2485 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:value> <span class="type">
2486 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:decimal</span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:value> <span class="occurs">[0..1]</span>
2487 </div></...></div>
2489 <script type="text/javascript">
2491 setState('h517931443_xibox', true);
2495 <div class="sample box">
2497 <input type="button" id="h517931443_diagram_button" class="control"
2498 onclick="switchState('h517931443_diagram'); return false;"
2499 style="display: none"/>
2500 <span class="caption">Diagram</span>
2502 <div id="h517931443_diagram" class="contents">
2503 <img usemap="#h169662420" src="schemaDiagrams/h169662420.png"/>
2505 Map ref: file:/D:/WORK/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester-atv/resources/phyloxml_schema/1.00//schemaDiagrams/h169662420.map--><map name="h169662420">
2508 <script type="text/javascript">
2510 setState('h517931443_diagram', true);
2514 <div class="schemaComponent box">
2516 <input type="button" id="h517931443_scbox_button" class="control"
2517 onclick="switchState('h517931443_scbox'); return false;"
2518 style="display: none"/>
2519 <span class="caption">Schema Component Representation</span>
2521 <div id="h517931443_scbox" class="contents">
2522 <div style="margin-left: 0em"><<span class="scTag">xs:complexType</span>
2523 <span class="scTag">name</span>="<span class="scContent">Date</span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:sequence</span>><div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
2524 <span class="scTag">name</span>="<span class="scContent">desc</span>" <span class="scTag">type</span>="<span class="scContent">
2526 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
2527 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>"/></div>
2528 <div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
2529 <span class="scTag">name</span>="<span class="scContent">value</span>" <span class="scTag">type</span>="<span class="scContent">
2531 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:decimal</span>
2532 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>"/></div></<span class="scTag">xs:sequence</span>></div>
2533 <div style="margin-left: 1.5em"><<span class="scTag">xs:attribute</span>
2534 <span class="scTag">name</span>="<span class="scContent">unit</span>" <span class="scTag">type</span>="<span class="scContent">
2536 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
2538 <div style="margin-left: 1.5em"><<span class="scTag">xs:attribute</span>
2539 <span class="scTag">name</span>="<span class="scContent">range</span>" <span class="scTag">type</span>="<span class="scContent">
2541 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:decimal</span>
2542 </span>"/></div></<span class="scTag">xs:complexType</span>></div>
2544 <script type="text/javascript">
2546 setState('h517931443_scbox', false);
2550 <div style="text-align: right; clear: both;">
2551 <a href="#top">top</a>
2554 <h3>Complex Type: <a name="h-979596407" class="name">Distribution</a>
2556 <table class="hierarchy">
2558 <th>Super-types:</th>
2566 <table class="properties">
2569 <td>Distribution</td>
2572 <th>Used by (from the same schema document)</th>
2573 <td>Complex Type <b>
2574 <a href="#h-1124608460">Clade</a>
2580 <a title="Look up 'Abstract' in glossary" href="phyloxml.xsd.html#term_Abstract">Abstract</a>
2585 <th>Documentation</th>
2586 <td class="documentation"> The geographic distribution of the items of a clade (species, sequences), intended for
2587 phylogeographic applications. The location can be described either by free text in the 'desc' element and/or
2588 by the coordinates of one or more 'Points' (similar to the 'Point' element in Google's KML format) or by
2592 <div class="sample box">
2594 <input type="button" id="h-979596407_xibox_button" class="control"
2595 onclick="switchState('h-979596407_xibox'); return false;"
2596 style="display: none"/>
2597 <span class="caption">XML Instance Representation</span>
2599 <div id="h-979596407_xibox" class="contents">
2600 <div style="margin-left: 0em"><...> <br/>
2601 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:desc> <span class="type">
2602 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:desc> <span class="occurs">[0..1]</span>
2604 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:point> <span class="type">
2605 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Point" type definition." href="#h-1112505301">Point</a>
2606 </span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:point> <span class="occurs">[0..*]</span>
2608 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:polygon> <span class="type">
2609 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Polygon" type definition." href="#h332351765">Polygon</a>
2610 </span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:polygon> <span class="occurs">[0..*]</span>
2611 </div></...></div>
2613 <script type="text/javascript">
2615 setState('h-979596407_xibox', true);
2619 <div class="sample box">
2621 <input type="button" id="h-979596407_diagram_button" class="control"
2622 onclick="switchState('h-979596407_diagram'); return false;"
2623 style="display: none"/>
2624 <span class="caption">Diagram</span>
2626 <div id="h-979596407_diagram" class="contents">
2627 <img usemap="#h-265752642" src="schemaDiagrams/h-265752642.png"/>
2629 Map ref: file:/D:/WORK/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester-atv/resources/phyloxml_schema/1.00//schemaDiagrams/h-265752642.map--><map name="h-265752642">
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2631 href="phyloxml.xsd.html#h-1112505301"/>
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2638 <script type="text/javascript">
2640 setState('h-979596407_diagram', true);
2644 <div class="schemaComponent box">
2646 <input type="button" id="h-979596407_scbox_button" class="control"
2647 onclick="switchState('h-979596407_scbox'); return false;"
2648 style="display: none"/>
2649 <span class="caption">Schema Component Representation</span>
2651 <div id="h-979596407_scbox" class="contents">
2652 <div style="margin-left: 0em"><<span class="scTag">xs:complexType</span>
2653 <span class="scTag">name</span>="<span class="scContent">Distribution</span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:sequence</span>><div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
2654 <span class="scTag">name</span>="<span class="scContent">desc</span>" <span class="scTag">type</span>="<span class="scContent">
2656 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
2657 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>"/></div>
2658 <div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
2659 <span class="scTag">name</span>="<span class="scContent">point</span>" <span class="scTag">type</span>="<span class="scContent">
2661 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Point" type definition." href="#h-1112505301">Point</a>
2663 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>" <span class="scTag">maxOccurs</span>="<span class="scContent">unbounded</span>"/></div>
2664 <div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
2665 <span class="scTag">name</span>="<span class="scContent">polygon</span>" <span class="scTag">type</span>="<span class="scContent">
2667 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Polygon" type definition." href="#h332351765">Polygon</a>
2669 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>" <span class="scTag">maxOccurs</span>="<span class="scContent">unbounded</span>"/></div></<span class="scTag">xs:sequence</span>></div></<span class="scTag">xs:complexType</span>></div>
2671 <script type="text/javascript">
2673 setState('h-979596407_scbox', false);
2677 <div style="text-align: right; clear: both;">
2678 <a href="#top">top</a>
2681 <h3>Complex Type: <a name="h259010940" class="name">DomainArchitecture</a>
2683 <table class="hierarchy">
2685 <th>Super-types:</th>
2693 <table class="properties">
2696 <td>DomainArchitecture</td>
2699 <th>Used by (from the same schema document)</th>
2700 <td>Complex Type <b>
2701 <a href="#h-1794244794">Sequence</a>
2707 <a title="Look up 'Abstract' in glossary" href="phyloxml.xsd.html#term_Abstract">Abstract</a>
2712 <th>Documentation</th>
2713 <td class="documentation"> This is used describe the domain architecture of a protein. Attribute 'length' is the total
2714 length of the protein</td>
2717 <div class="sample box">
2719 <input type="button" id="h259010940_xibox_button" class="control"
2720 onclick="switchState('h259010940_xibox'); return false;"
2721 style="display: none"/>
2722 <span class="caption">XML Instance Representation</span>
2724 <div id="h259010940_xibox" class="contents">
2725 <div style="margin-left: 0em"><...<br/>
2726 <span style="margin-left: 0.5em"> length="<span class="type">
2727 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:nonNegativeInteger</span>
2728 <span class="occurs">[0..1]</span>"</span>> <br/>
2729 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:domain> <span class="type">
2730 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "ProteinDomain" type definition." href="#h-1389097534">ProteinDomain</a>
2731 </span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:domain> <span class="occurs">[1..*]</span>
2732 </div></...></div>
2734 <script type="text/javascript">
2736 setState('h259010940_xibox', true);
2740 <div class="sample box">
2742 <input type="button" id="h259010940_diagram_button" class="control"
2743 onclick="switchState('h259010940_diagram'); return false;"
2744 style="display: none"/>
2745 <span class="caption">Diagram</span>
2747 <div id="h259010940_diagram" class="contents">
2748 <img usemap="#h-93417557" src="schemaDiagrams/h-93417557.png"/>
2750 Map ref: file:/D:/WORK/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester-atv/resources/phyloxml_schema/1.00//schemaDiagrams/h-93417557.map--><map name="h-93417557">
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2752 href="phyloxml.xsd.html#h-1389097534"/>
2756 <script type="text/javascript">
2758 setState('h259010940_diagram', true);
2762 <div class="schemaComponent box">
2764 <input type="button" id="h259010940_scbox_button" class="control"
2765 onclick="switchState('h259010940_scbox'); return false;"
2766 style="display: none"/>
2767 <span class="caption">Schema Component Representation</span>
2769 <div id="h259010940_scbox" class="contents">
2770 <div style="margin-left: 0em"><<span class="scTag">xs:complexType</span>
2771 <span class="scTag">name</span>="<span class="scContent">DomainArchitecture</span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:sequence</span>><div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
2772 <span class="scTag">name</span>="<span class="scContent">domain</span>" <span class="scTag">type</span>="<span class="scContent">
2774 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "ProteinDomain" type definition." href="#h-1389097534">ProteinDomain</a>
2776 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">1</span>" <span class="scTag">maxOccurs</span>="<span class="scContent">unbounded</span>"/></div></<span class="scTag">xs:sequence</span>></div>
2777 <div style="margin-left: 1.5em"><<span class="scTag">xs:attribute</span>
2778 <span class="scTag">name</span>="<span class="scContent">length</span>" <span class="scTag">type</span>="<span class="scContent">
2780 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:nonNegativeInteger</span>
2781 </span>"/></div></<span class="scTag">xs:complexType</span>></div>
2783 <script type="text/javascript">
2785 setState('h259010940_scbox', false);
2789 <div style="text-align: right; clear: both;">
2790 <a href="#top">top</a>
2793 <h3>Complex Type: <a name="h-436501026" class="name">Events</a>
2795 <table class="hierarchy">
2797 <th>Super-types:</th>
2805 <table class="properties">
2811 <th>Used by (from the same schema document)</th>
2812 <td>Complex Type <b>
2813 <a href="#h-1124608460">Clade</a>
2819 <a title="Look up 'Abstract' in glossary" href="phyloxml.xsd.html#term_Abstract">Abstract</a>
2824 <th>Documentation</th>
2825 <td class="documentation"> Events at the root node of a clade (e.g. one gene duplication). </td>
2828 <div class="sample box">
2830 <input type="button" id="h-436501026_xibox_button" class="control"
2831 onclick="switchState('h-436501026_xibox'); return false;"
2832 style="display: none"/>
2833 <span class="caption">XML Instance Representation</span>
2835 <div id="h-436501026_xibox" class="contents">
2836 <div style="margin-left: 0em"><...> <br/>
2837 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:type> <span class="type">
2838 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "EventType" type definition." href="#h1358103055">EventType</a>
2839 </span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:type> <span class="occurs">[0..1]</span>
2841 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:duplications> <span class="type">
2842 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:nonNegativeInteger</span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:duplications> <span class="occurs">[0..1]</span>
2844 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:speciations> <span class="type">
2845 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:nonNegativeInteger</span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:speciations> <span class="occurs">[0..1]</span>
2847 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:losses> <span class="type">
2848 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:nonNegativeInteger</span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:losses> <span class="occurs">[0..1]</span>
2850 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:confidence> <span class="type">
2851 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Confidence" type definition." href="#h-993584945">Confidence</a>
2852 </span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:confidence> <span class="occurs">[0..1]</span>
2853 </div></...></div>
2855 <script type="text/javascript">
2857 setState('h-436501026_xibox', true);
2861 <div class="sample box">
2863 <input type="button" id="h-436501026_diagram_button" class="control"
2864 onclick="switchState('h-436501026_diagram'); return false;"
2865 style="display: none"/>
2866 <span class="caption">Diagram</span>
2868 <div id="h-436501026_diagram" class="contents">
2869 <img usemap="#h-1724830583" src="schemaDiagrams/h-1724830583.png"/>
2871 Map ref: file:/D:/WORK/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester-atv/resources/phyloxml_schema/1.00//schemaDiagrams/h-1724830583.map--><map name="h-1724830583">
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2873 href="phyloxml.xsd.html#h1358103055"/>
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2876 href="phyloxml.xsd.html#h-993584945"/>
2880 <script type="text/javascript">
2882 setState('h-436501026_diagram', true);
2886 <div class="schemaComponent box">
2888 <input type="button" id="h-436501026_scbox_button" class="control"
2889 onclick="switchState('h-436501026_scbox'); return false;"
2890 style="display: none"/>
2891 <span class="caption">Schema Component Representation</span>
2893 <div id="h-436501026_scbox" class="contents">
2894 <div style="margin-left: 0em"><<span class="scTag">xs:complexType</span>
2895 <span class="scTag">name</span>="<span class="scContent">Events</span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:sequence</span>><div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
2896 <span class="scTag">name</span>="<span class="scContent">type</span>" <span class="scTag">type</span>="<span class="scContent">
2898 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "EventType" type definition." href="#h1358103055">EventType</a>
2900 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>"/></div>
2901 <div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
2902 <span class="scTag">name</span>="<span class="scContent">duplications</span>" <span class="scTag">type</span>="<span class="scContent">
2904 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:nonNegativeInteger</span>
2905 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>"/></div>
2906 <div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
2907 <span class="scTag">name</span>="<span class="scContent">speciations</span>" <span class="scTag">type</span>="<span class="scContent">
2909 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:nonNegativeInteger</span>
2910 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>"/></div>
2911 <div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
2912 <span class="scTag">name</span>="<span class="scContent">losses</span>" <span class="scTag">type</span>="<span class="scContent">
2914 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:nonNegativeInteger</span>
2915 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>"/></div>
2916 <div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
2917 <span class="scTag">name</span>="<span class="scContent">confidence</span>" <span class="scTag">type</span>="<span class="scContent">
2919 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Confidence" type definition." href="#h-993584945">Confidence</a>
2921 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>"/></div></<span class="scTag">xs:sequence</span>></div></<span class="scTag">xs:complexType</span>></div>
2923 <script type="text/javascript">
2925 setState('h-436501026_scbox', false);
2929 <div style="text-align: right; clear: both;">
2930 <a href="#top">top</a>
2933 <h3>Complex Type: <a name="h-853091232" class="name">Id</a>
2935 <table class="hierarchy">
2937 <th>Super-types:</th>
2940 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span> < <strong>Id</strong> (by extension)</td>
2947 <table class="properties">
2953 <th>Used by (from the same schema document)</th>
2954 <td>Complex Type <b>
2955 <a href="#h535307528">Phylogeny</a>
2956 </b>, Complex Type <b>
2957 <a href="#h-1124608460">Clade</a>
2958 </b>, Complex Type <b>
2959 <a href="#h888650454">Taxonomy</a>
2965 <a title="Look up 'Abstract' in glossary" href="phyloxml.xsd.html#term_Abstract">Abstract</a>
2970 <th>Documentation</th>
2971 <td class="documentation"> A general purpose identifier element. Allows to indicate the type (or source) of an
2975 <div class="sample box">
2977 <input type="button" id="h-853091232_xibox_button" class="control"
2978 onclick="switchState('h-853091232_xibox'); return false;"
2979 style="display: none"/>
2980 <span class="caption">XML Instance Representation</span>
2982 <div id="h-853091232_xibox" class="contents">
2983 <div style="margin-left: 0em"><...<br/>
2984 <span style="margin-left: 0.5em" class="newFields"> type="<span class="type">
2985 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
2986 <span class="occurs">[0..1]</span>"</span>> <br/>
2987 <span style="margin-left: 1.5em">
2989 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
2991 <br/></...></div>
2993 <script type="text/javascript">
2995 setState('h-853091232_xibox', true);
2999 <div class="sample box">
3001 <input type="button" id="h-853091232_diagram_button" class="control"
3002 onclick="switchState('h-853091232_diagram'); return false;"
3003 style="display: none"/>
3004 <span class="caption">Diagram</span>
3006 <div id="h-853091232_diagram" class="contents">
3007 <img usemap="#h-1484760249" src="schemaDiagrams/h-1484760249.png"/>
3009 Map ref: file:/D:/WORK/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester-atv/resources/phyloxml_schema/1.00//schemaDiagrams/h-1484760249.map--><map name="h-1484760249">
3012 <script type="text/javascript">
3014 setState('h-853091232_diagram', true);
3018 <div class="schemaComponent box">
3020 <input type="button" id="h-853091232_scbox_button" class="control"
3021 onclick="switchState('h-853091232_scbox'); return false;"
3022 style="display: none"/>
3023 <span class="caption">Schema Component Representation</span>
3025 <div id="h-853091232_scbox" class="contents">
3026 <div style="margin-left: 0em"><<span class="scTag">xs:complexType</span>
3027 <span class="scTag">name</span>="<span class="scContent">Id</span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:simpleContent</span>><div style="margin-left: 1.5em"><<span class="scTag">xs:extension</span>
3028 <span class="scTag">base</span>="<span class="scContent">
3030 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
3031 </span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:attribute</span>
3032 <span class="scTag">name</span>="<span class="scContent">type</span>" <span class="scTag">type</span>="<span class="scContent">
3034 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
3035 </span>"/></div></<span class="scTag">xs:extension</span>></div></<span class="scTag">xs:simpleContent</span>></div></<span class="scTag">xs:complexType</span>></div>
3037 <script type="text/javascript">
3039 setState('h-853091232_scbox', false);
3043 <div style="text-align: right; clear: both;">
3044 <a href="#top">top</a>
3047 <h3>Complex Type: <a name="h535307528" class="name">Phylogeny</a>
3049 <table class="hierarchy">
3051 <th>Super-types:</th>
3059 <table class="properties">
3065 <th>Used by (from the same schema document)</th>
3066 <td>Complex Type <b>
3067 <a href="#h155831896">Phyloxml</a>
3073 <a title="Look up 'Abstract' in glossary" href="phyloxml.xsd.html#term_Abstract">Abstract</a>
3078 <th>Documentation</th>
3079 <td class="documentation"> Element Phylogeny is used to represent a phylogeny. The required attribute 'rooted' is used
3080 to indicate whether the phylogeny is rooted or not. The attribute 'rerootable' can be used to indicate that
3081 the phylogeny is not allowed to be rooted differently (i.e. because it is associated with root dependent
3082 data, such as gene duplications). The attribute 'type' can be used to indicate the type of phylogeny (i.e.
3083 'gene tree'). It is recommended to use the attribute 'branch_length_unit' if the phylogeny has branch
3084 lengths. Element clade is used in a recursive manner to describe the topology of a phylogenetic
3088 <div class="sample box">
3090 <input type="button" id="h535307528_xibox_button" class="control"
3091 onclick="switchState('h535307528_xibox'); return false;"
3092 style="display: none"/>
3093 <span class="caption">XML Instance Representation</span>
3095 <div id="h535307528_xibox" class="contents">
3096 <div style="margin-left: 0em"><...<br/>
3097 <span style="margin-left: 0.5em"> rooted="<span class="type">
3098 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:boolean</span>
3099 <span class="occurs">[1]</span>"</span>
3101 <span style="margin-left: 0.5em"> rerootable="<span class="type">
3102 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:boolean</span>
3103 <span class="occurs">[0..1]</span>"</span>
3105 <span style="margin-left: 0.5em"> branch_length_unit="<span class="type">
3106 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
3107 <span class="occurs">[0..1]</span>"</span>
3109 <span style="margin-left: 0.5em"> type="<span class="type">
3110 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
3111 <span class="occurs">[0..1]</span>"</span>> <br/>
3112 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:name> <span class="type">
3113 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:name> <span class="occurs">[0..1]</span>
3115 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:id> <span class="type">
3116 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Id" type definition." href="#h-853091232">Id</a>
3117 </span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:id> <span class="occurs">[0..1]</span>
3119 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:description> <span class="type">
3120 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:description> <span class="occurs">[0..1]</span>
3122 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:date> <span class="type">
3123 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:dateTime</span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:date> <span class="occurs">[0..1]</span>
3125 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:confidence> <span class="type">
3126 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Confidence" type definition." href="#h-993584945">Confidence</a>
3127 </span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:confidence> <span class="occurs">[0..*]</span>
3129 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:clade> <span class="type">
3130 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Clade" type definition." href="#h-1124608460">Clade</a>
3131 </span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:clade> <span class="occurs">[0..1]</span>
3133 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:clade_relation> <span class="type">
3134 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "CladeRelation" type definition." href="#h192331856">CladeRelation</a>
3135 </span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:clade_relation> <span class="occurs">[0..*]</span>
3137 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:sequence_relation> <span class="type">
3138 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "SequenceRelation" type definition." href="#h-802965662">SequenceRelation</a>
3139 </span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:sequence_relation> <span class="occurs">[0..*]</span>
3141 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:property> <span class="type">
3142 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Property" type definition." href="#h158033242">Property</a>
3143 </span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:property> <span class="occurs">[0..*]</span>
3145 <div class="other" style="margin-left: 1.5em">Allow any elements from a namespace other than this schema's namespace (lax validation). <span class="occurs">[0..*]</span>
3146 </div></...></div>
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3159 <span class="caption">Diagram</span>
3161 <div id="h535307528_diagram" class="contents">
3162 <img usemap="#h731810719" src="schemaDiagrams/h731810719.png"/>
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3185 <script type="text/javascript">
3187 setState('h535307528_diagram', true);
3191 <div class="schemaComponent box">
3193 <input type="button" id="h535307528_scbox_button" class="control"
3194 onclick="switchState('h535307528_scbox'); return false;"
3195 style="display: none"/>
3196 <span class="caption">Schema Component Representation</span>
3198 <div id="h535307528_scbox" class="contents">
3199 <div style="margin-left: 0em"><<span class="scTag">xs:complexType</span>
3200 <span class="scTag">name</span>="<span class="scContent">Phylogeny</span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:sequence</span>><div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
3201 <span class="scTag">name</span>="<span class="scContent">name</span>" <span class="scTag">type</span>="<span class="scContent">
3203 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
3204 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>"/></div>
3205 <div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
3206 <span class="scTag">name</span>="<span class="scContent">id</span>" <span class="scTag">type</span>="<span class="scContent">
3208 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Id" type definition." href="#h-853091232">Id</a>
3210 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>"/></div>
3211 <div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
3212 <span class="scTag">name</span>="<span class="scContent">description</span>" <span class="scTag">type</span>="<span class="scContent">
3214 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
3215 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>"/></div>
3216 <div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
3217 <span class="scTag">name</span>="<span class="scContent">date</span>" <span class="scTag">type</span>="<span class="scContent">
3219 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:dateTime</span>
3220 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>"/></div>
3221 <div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
3222 <span class="scTag">name</span>="<span class="scContent">confidence</span>" <span class="scTag">type</span>="<span class="scContent">
3224 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Confidence" type definition." href="#h-993584945">Confidence</a>
3226 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>" <span class="scTag">maxOccurs</span>="<span class="scContent">unbounded</span>"/></div>
3227 <div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
3228 <span class="scTag">name</span>="<span class="scContent">clade</span>" <span class="scTag">type</span>="<span class="scContent">
3230 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Clade" type definition." href="#h-1124608460">Clade</a>
3232 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>"/></div>
3233 <div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
3234 <span class="scTag">name</span>="<span class="scContent">clade_relation</span>" <span class="scTag">type</span>="<span class="scContent">
3236 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "CladeRelation" type definition." href="#h192331856">CladeRelation</a>
3238 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>" <span class="scTag">maxOccurs</span>="<span class="scContent">unbounded</span>"/></div>
3239 <div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
3240 <span class="scTag">name</span>="<span class="scContent">sequence_relation</span>" <span class="scTag">type</span>="<span class="scContent">
3242 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "SequenceRelation" type definition." href="#h-802965662">SequenceRelation</a>
3244 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>" <span class="scTag">maxOccurs</span>="<span class="scContent">unbounded</span>"/></div>
3245 <div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
3246 <span class="scTag">name</span>="<span class="scContent">property</span>" <span class="scTag">type</span>="<span class="scContent">
3248 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Property" type definition." href="#h158033242">Property</a>
3250 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>" <span class="scTag">maxOccurs</span>="<span class="scContent">unbounded</span>"/></div>
3251 <div style="margin-left: 1.5em"><<span class="scTag">xs:any</span>
3252 <span class="scTag">minOccurs</span>="<span class="scContent">0</span>" <span class="scTag">maxOccurs</span>="<span class="scContent">unbounded</span>" <span class="scTag">processContents</span>="<span class="scContent">lax</span>" <span class="scTag">namespace</span>="<span class="scContent">##other</span>"/></div></<span class="scTag">xs:sequence</span>></div>
3253 <div style="margin-left: 1.5em"><<span class="scTag">xs:attribute</span>
3254 <span class="scTag">name</span>="<span class="scContent">rooted</span>" <span class="scTag">type</span>="<span class="scContent">
3256 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:boolean</span>
3257 </span>" <span class="scTag">use</span>="<span class="scContent">required</span>"/></div>
3258 <div style="margin-left: 1.5em"><<span class="scTag">xs:attribute</span>
3259 <span class="scTag">name</span>="<span class="scContent">rerootable</span>" <span class="scTag">type</span>="<span class="scContent">
3261 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:boolean</span>
3263 <div style="margin-left: 1.5em"><<span class="scTag">xs:attribute</span>
3264 <span class="scTag">name</span>="<span class="scContent">branch_length_unit</span>" <span class="scTag">type</span>="<span class="scContent">
3266 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
3268 <div style="margin-left: 1.5em"><<span class="scTag">xs:attribute</span>
3269 <span class="scTag">name</span>="<span class="scContent">type</span>" <span class="scTag">type</span>="<span class="scContent">
3271 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
3272 </span>"/></div></<span class="scTag">xs:complexType</span>></div>
3274 <script type="text/javascript">
3276 setState('h535307528_scbox', false);
3280 <div style="text-align: right; clear: both;">
3281 <a href="#top">top</a>
3284 <h3>Complex Type: <a name="h155831896" class="name">Phyloxml</a>
3286 <table class="hierarchy">
3288 <th>Super-types:</th>
3296 <table class="properties">
3302 <th>Used by (from the same schema document)</th>
3304 <a href="#h270234806">phyloxml</a>
3310 <a title="Look up 'Abstract' in glossary" href="phyloxml.xsd.html#term_Abstract">Abstract</a>
3315 <th>Documentation</th>
3316 <td class="documentation"> 'phyloxml' is the name of the root element. Phyloxml contains an arbitrary number of
3317 'phylogeny' elements (each representing one phylogeny) possibly followed by elements from other namespaces.
3321 <div class="sample box">
3323 <input type="button" id="h155831896_xibox_button" class="control"
3324 onclick="switchState('h155831896_xibox'); return false;"
3325 style="display: none"/>
3326 <span class="caption">XML Instance Representation</span>
3328 <div id="h155831896_xibox" class="contents">
3329 <div style="margin-left: 0em"><...> <br/>
3330 <span class="group" style="margin-left: 1.5em">Start <a title="Look up 'Sequence' in glossary" href="phyloxml.xsd.html#term_Sequence">Sequence</a>
3331 <span class="occurs">[1..*]</span>
3334 <div style="margin-left: 3em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:phylogeny> <span class="type">
3335 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Phylogeny" type definition." href="#h535307528">Phylogeny</a>
3336 </span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:phylogeny> <span class="occurs">[0..*]</span>
3338 <div class="other" style="margin-left: 3em">Allow any elements from a namespace other than this schema's namespace (lax validation). <span class="occurs">[0..*]</span>
3340 <span class="group" style="margin-left: 1.5em">End Sequence</span>
3341 <br/></...></div>
3343 <script type="text/javascript">
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3352 onclick="switchState('h155831896_diagram'); return false;"
3353 style="display: none"/>
3354 <span class="caption">Diagram</span>
3356 <div id="h155831896_diagram" class="contents">
3357 <img usemap="#h-354757553" src="schemaDiagrams/h-354757553.png"/>
3359 Map ref: file:/D:/WORK/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester-atv/resources/phyloxml_schema/1.00//schemaDiagrams/h-354757553.map--><map name="h-354757553">
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3374 onclick="switchState('h155831896_scbox'); return false;"
3375 style="display: none"/>
3376 <span class="caption">Schema Component Representation</span>
3378 <div id="h155831896_scbox" class="contents">
3379 <div style="margin-left: 0em"><<span class="scTag">xs:complexType</span>
3380 <span class="scTag">name</span>="<span class="scContent">Phyloxml</span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:sequence</span>
3381 <span class="scTag">maxOccurs</span>="<span class="scContent">unbounded</span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
3382 <span class="scTag">name</span>="<span class="scContent">phylogeny</span>" <span class="scTag">type</span>="<span class="scContent">
3384 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Phylogeny" type definition." href="#h535307528">Phylogeny</a>
3386 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>" <span class="scTag">maxOccurs</span>="<span class="scContent">unbounded</span>"/></div>
3387 <div style="margin-left: 1.5em"><<span class="scTag">xs:any</span>
3388 <span class="scTag">minOccurs</span>="<span class="scContent">0</span>" <span class="scTag">maxOccurs</span>="<span class="scContent">unbounded</span>" <span class="scTag">processContents</span>="<span class="scContent">lax</span>" <span class="scTag">namespace</span>="<span class="scContent">##other</span>"/></div></<span class="scTag">xs:sequence</span>></div></<span class="scTag">xs:complexType</span>></div>
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3396 <div style="text-align: right; clear: both;">
3397 <a href="#top">top</a>
3400 <h3>Complex Type: <a name="h-1112505301" class="name">Point</a>
3402 <table class="hierarchy">
3404 <th>Super-types:</th>
3412 <table class="properties">
3418 <th>Used by (from the same schema document)</th>
3419 <td>Complex Type <b>
3420 <a href="#h-979596407">Distribution</a>
3421 </b>, Complex Type <b>
3422 <a href="#h332351765">Polygon</a>
3428 <a title="Look up 'Abstract' in glossary" href="phyloxml.xsd.html#term_Abstract">Abstract</a>
3433 <th>Documentation</th>
3434 <td class="documentation"> The coordinates of a point with an optional altitude (used by element 'Distribution').
3435 Required attribute 'geodetic_datum' is used to indicate the geodetic datum (also called 'map datum'), for
3436 example Google's KML uses 'WGS84'. </td>
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3442 onclick="switchState('h-1112505301_xibox'); return false;"
3443 style="display: none"/>
3444 <span class="caption">XML Instance Representation</span>
3446 <div id="h-1112505301_xibox" class="contents">
3447 <div style="margin-left: 0em"><...<br/>
3448 <span style="margin-left: 0.5em"> geodetic_datum="<span class="type">
3449 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
3450 <span class="occurs">[1]</span>"</span>> <br/>
3451 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:lat> <span class="type">
3452 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:decimal</span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:lat> <span class="occurs">[1]</span>
3454 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:long> <span class="type">
3455 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:decimal</span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:long> <span class="occurs">[1]</span>
3457 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:alt> <span class="type">
3458 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:decimal</span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:alt> <span class="occurs">[0..1]</span>
3459 </div></...></div>
3461 <script type="text/javascript">
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3469 <input type="button" id="h-1112505301_diagram_button" class="control"
3470 onclick="switchState('h-1112505301_diagram'); return false;"
3471 style="display: none"/>
3472 <span class="caption">Diagram</span>
3474 <div id="h-1112505301_diagram" class="contents">
3475 <img usemap="#h2137002076" src="schemaDiagrams/h2137002076.png"/>
3477 Map ref: file:/D:/WORK/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester-atv/resources/phyloxml_schema/1.00//schemaDiagrams/h2137002076.map--><map name="h2137002076">
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3491 <span class="caption">Schema Component Representation</span>
3493 <div id="h-1112505301_scbox" class="contents">
3494 <div style="margin-left: 0em"><<span class="scTag">xs:complexType</span>
3495 <span class="scTag">name</span>="<span class="scContent">Point</span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:sequence</span>><div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
3496 <span class="scTag">name</span>="<span class="scContent">lat</span>" <span class="scTag">type</span>="<span class="scContent">
3498 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:decimal</span>
3500 <div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
3501 <span class="scTag">name</span>="<span class="scContent">long</span>" <span class="scTag">type</span>="<span class="scContent">
3503 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:decimal</span>
3505 <div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
3506 <span class="scTag">name</span>="<span class="scContent">alt</span>" <span class="scTag">type</span>="<span class="scContent">
3508 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:decimal</span>
3509 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>"/></div></<span class="scTag">xs:sequence</span>></div>
3510 <div style="margin-left: 1.5em"><<span class="scTag">xs:attribute</span>
3511 <span class="scTag">name</span>="<span class="scContent">geodetic_datum</span>" <span class="scTag">type</span>="<span class="scContent">
3513 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
3514 </span>" <span class="scTag">use</span>="<span class="scContent">required</span>"/></div></<span class="scTag">xs:complexType</span>></div>
3516 <script type="text/javascript">
3518 setState('h-1112505301_scbox', false);
3522 <div style="text-align: right; clear: both;">
3523 <a href="#top">top</a>
3526 <h3>Complex Type: <a name="h332351765" class="name">Polygon</a>
3528 <table class="hierarchy">
3530 <th>Super-types:</th>
3538 <table class="properties">
3544 <th>Used by (from the same schema document)</th>
3545 <td>Complex Type <b>
3546 <a href="#h-979596407">Distribution</a>
3552 <a title="Look up 'Abstract' in glossary" href="phyloxml.xsd.html#term_Abstract">Abstract</a>
3557 <th>Documentation</th>
3558 <td class="documentation"> A polygon defined by a list of 'Points' (used by element 'Distribution').
3562 <div class="sample box">
3564 <input type="button" id="h332351765_xibox_button" class="control"
3565 onclick="switchState('h332351765_xibox'); return false;"
3566 style="display: none"/>
3567 <span class="caption">XML Instance Representation</span>
3569 <div id="h332351765_xibox" class="contents">
3570 <div style="margin-left: 0em"><...> <br/>
3571 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:point> <span class="type">
3572 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Point" type definition." href="#h-1112505301">Point</a>
3573 </span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:point> <span class="occurs">[3..*]</span>
3574 </div></...></div>
3576 <script type="text/javascript">
3578 setState('h332351765_xibox', true);
3582 <div class="sample box">
3584 <input type="button" id="h332351765_diagram_button" class="control"
3585 onclick="switchState('h332351765_diagram'); return false;"
3586 style="display: none"/>
3587 <span class="caption">Diagram</span>
3589 <div id="h332351765_diagram" class="contents">
3590 <img usemap="#h555770290" src="schemaDiagrams/h555770290.png"/>
3592 Map ref: file:/D:/WORK/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester-atv/resources/phyloxml_schema/1.00//schemaDiagrams/h555770290.map--><map name="h555770290">
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3598 <script type="text/javascript">
3600 setState('h332351765_diagram', true);
3604 <div class="schemaComponent box">
3606 <input type="button" id="h332351765_scbox_button" class="control"
3607 onclick="switchState('h332351765_scbox'); return false;"
3608 style="display: none"/>
3609 <span class="caption">Schema Component Representation</span>
3611 <div id="h332351765_scbox" class="contents">
3612 <div style="margin-left: 0em"><<span class="scTag">xs:complexType</span>
3613 <span class="scTag">name</span>="<span class="scContent">Polygon</span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:sequence</span>><div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
3614 <span class="scTag">name</span>="<span class="scContent">point</span>" <span class="scTag">type</span>="<span class="scContent">
3616 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Point" type definition." href="#h-1112505301">Point</a>
3618 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">3</span>" <span class="scTag">maxOccurs</span>="<span class="scContent">unbounded</span>"/></div></<span class="scTag">xs:sequence</span>></div></<span class="scTag">xs:complexType</span>></div>
3620 <script type="text/javascript">
3622 setState('h332351765_scbox', false);
3626 <div style="text-align: right; clear: both;">
3627 <a href="#top">top</a>
3630 <h3>Complex Type: <a name="h158033242" class="name">Property</a>
3632 <table class="hierarchy">
3634 <th>Super-types:</th>
3642 <table class="properties">
3648 <th>Used by (from the same schema document)</th>
3649 <td>Complex Type <b>
3650 <a href="#h535307528">Phylogeny</a>
3651 </b>, Complex Type <b>
3652 <a href="#h-1124608460">Clade</a>
3653 </b>, Complex Type <b>
3654 <a href="#h917087604">Annotation</a>
3660 <a title="Look up 'Abstract' in glossary" href="phyloxml.xsd.html#term_Abstract">Abstract</a>
3665 <th>Documentation</th>
3666 <td class="documentation"> Property allows for typed and referenced properties from external resources to be attached
3667 to 'Phylogeny', 'Clade', and 'Annotation'. The value of a property is its mixed (free text) content.
3668 Attribute 'datatype' indicates the type of a property and is limited to xsd-datatypes (e.g. 'xsd:string',
3669 'xsd:boolean', 'xsd:integer', 'xsd:decimal', 'xsd:float', 'xsd:double', 'xsd:date', 'xsd:anyURI'). Attribute
3670 'applies_to' indicates the item to which a property applies to (e.g. 'node' for the parent node of a clade,
3671 'parent_branch' for the parent branch of a clade). Attribute 'id_ref' allows to attached a property
3672 specifically to one element (on the xml-level). Optional attribute 'unit' is used to indicate the unit of
3673 the property. An example: <property datatype="xsd:integer" ref="NOAA:depth" applies_to="clade"
3674 unit="METRIC:m"> 200 </property> </td>
3677 <div class="sample box">
3679 <input type="button" id="h158033242_xibox_button" class="control"
3680 onclick="switchState('h158033242_xibox'); return false;"
3681 style="display: none"/>
3682 <span class="caption">XML Instance Representation</span>
3684 <div id="h158033242_xibox" class="contents">
3685 <div style="margin-left: 0em"><...<br/>
3686 <span style="margin-left: 0.5em"> ref="<span class="type">
3687 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "ref" type definition." href="#h-675984882">ref</a>
3689 <span class="occurs">[1]</span>"</span>
3691 <span style="margin-left: 0.5em"> unit="<span class="type">
3692 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "ref" type definition." href="#h-675984882">ref</a>
3694 <span class="occurs">[0..1]</span>"</span>
3696 <span style="margin-left: 0.5em"> datatype="<span class="type">
3697 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "PropertyDataType" type definition." href="#h-54338178">PropertyDataType</a>
3699 <span class="occurs">[1]</span>"</span>
3701 <span style="margin-left: 0.5em"> applies_to="<span class="type">
3702 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "AppliesTo" type definition." href="#h-763252414">AppliesTo</a>
3704 <span class="occurs">[1]</span>"</span>
3706 <span style="margin-left: 0.5em"> id_ref="<span class="type">
3707 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "id_ref" type definition." href="#h577349652">id_ref</a>
3709 <span class="occurs">[0..1]</span>"</span>/> </div>
3711 <script type="text/javascript">
3713 setState('h158033242_xibox', true);
3717 <div class="sample box">
3719 <input type="button" id="h158033242_diagram_button" class="control"
3720 onclick="switchState('h158033242_diagram'); return false;"
3721 style="display: none"/>
3722 <span class="caption">Diagram</span>
3724 <div id="h158033242_diagram" class="contents">
3725 <img usemap="#h-411495795" src="schemaDiagrams/h-411495795.png"/>
3727 Map ref: file:/D:/WORK/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester-atv/resources/phyloxml_schema/1.00//schemaDiagrams/h-411495795.map--><map name="h-411495795">
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3751 <div class="schemaComponent box">
3753 <input type="button" id="h158033242_scbox_button" class="control"
3754 onclick="switchState('h158033242_scbox'); return false;"
3755 style="display: none"/>
3756 <span class="caption">Schema Component Representation</span>
3758 <div id="h158033242_scbox" class="contents">
3759 <div style="margin-left: 0em"><<span class="scTag">xs:complexType</span>
3760 <span class="scTag">name</span>="<span class="scContent">Property</span>" <span class="scTag">mixed</span>="<span class="scContent">true</span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:attribute</span>
3761 <span class="scTag">name</span>="<span class="scContent">ref</span>" <span class="scTag">type</span>="<span class="scContent">
3763 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "ref" type definition." href="#h-675984882">ref</a>
3765 </span>" <span class="scTag">use</span>="<span class="scContent">required</span>"/></div>
3766 <div style="margin-left: 1.5em"><<span class="scTag">xs:attribute</span>
3767 <span class="scTag">name</span>="<span class="scContent">unit</span>" <span class="scTag">type</span>="<span class="scContent">
3769 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "ref" type definition." href="#h-675984882">ref</a>
3772 <div style="margin-left: 1.5em"><<span class="scTag">xs:attribute</span>
3773 <span class="scTag">name</span>="<span class="scContent">datatype</span>" <span class="scTag">type</span>="<span class="scContent">
3775 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "PropertyDataType" type definition." href="#h-54338178">PropertyDataType</a>
3777 </span>" <span class="scTag">use</span>="<span class="scContent">required</span>"/></div>
3778 <div style="margin-left: 1.5em"><<span class="scTag">xs:attribute</span>
3779 <span class="scTag">name</span>="<span class="scContent">applies_to</span>" <span class="scTag">type</span>="<span class="scContent">
3781 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "AppliesTo" type definition." href="#h-763252414">AppliesTo</a>
3783 </span>" <span class="scTag">use</span>="<span class="scContent">required</span>"/></div>
3784 <div style="margin-left: 1.5em"><<span class="scTag">xs:attribute</span>
3785 <span class="scTag">name</span>="<span class="scContent">id_ref</span>" <span class="scTag">type</span>="<span class="scContent">
3787 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "id_ref" type definition." href="#h577349652">id_ref</a>
3789 </span>"/></div></<span class="scTag">xs:complexType</span>></div>
3791 <script type="text/javascript">
3793 setState('h158033242_scbox', false);
3797 <div style="text-align: right; clear: both;">
3798 <a href="#top">top</a>
3801 <h3>Complex Type: <a name="h-1389097534" class="name">ProteinDomain</a>
3803 <table class="hierarchy">
3805 <th>Super-types:</th>
3808 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span> < <strong>ProteinDomain</strong> (by extension)</td>
3815 <table class="properties">
3818 <td>ProteinDomain</td>
3821 <th>Used by (from the same schema document)</th>
3822 <td>Complex Type <b>
3823 <a href="#h259010940">DomainArchitecture</a>
3829 <a title="Look up 'Abstract' in glossary" href="phyloxml.xsd.html#term_Abstract">Abstract</a>
3834 <th>Documentation</th>
3835 <td class="documentation"> To represent an individual domain in a domain architecture. The name/unique identifier is
3836 described via the 'id' attribute. 'confidence' can be used to store (i.e.) E-values.</td>
3839 <div class="sample box">
3841 <input type="button" id="h-1389097534_xibox_button" class="control"
3842 onclick="switchState('h-1389097534_xibox'); return false;"
3843 style="display: none"/>
3844 <span class="caption">XML Instance Representation</span>
3846 <div id="h-1389097534_xibox" class="contents">
3847 <div style="margin-left: 0em"><...<br/>
3848 <span style="margin-left: 0.5em" class="newFields"> from="<span class="type">
3849 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:nonNegativeInteger</span>
3850 <span class="occurs">[1]</span>"</span>
3852 <span style="margin-left: 0.5em" class="newFields"> to="<span class="type">
3853 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:nonNegativeInteger</span>
3854 <span class="occurs">[1]</span>"</span>
3856 <span style="margin-left: 0.5em" class="newFields"> confidence="<span class="type">
3857 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:double</span>
3858 <span class="occurs">[0..1]</span>"</span>
3860 <span style="margin-left: 0.5em" class="newFields"> id="<span class="type">
3861 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
3862 <span class="occurs">[0..1]</span>"</span>> <br/>
3863 <span style="margin-left: 1.5em">
3865 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
3867 <br/></...></div>
3869 <script type="text/javascript">
3871 setState('h-1389097534_xibox', true);
3875 <div class="sample box">
3877 <input type="button" id="h-1389097534_diagram_button" class="control"
3878 onclick="switchState('h-1389097534_diagram'); return false;"
3879 style="display: none"/>
3880 <span class="caption">Diagram</span>
3882 <div id="h-1389097534_diagram" class="contents">
3883 <img usemap="#h1501379365" src="schemaDiagrams/h1501379365.png"/>
3885 Map ref: file:/D:/WORK/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester-atv/resources/phyloxml_schema/1.00//schemaDiagrams/h1501379365.map--><map name="h1501379365">
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3894 <div class="schemaComponent box">
3896 <input type="button" id="h-1389097534_scbox_button" class="control"
3897 onclick="switchState('h-1389097534_scbox'); return false;"
3898 style="display: none"/>
3899 <span class="caption">Schema Component Representation</span>
3901 <div id="h-1389097534_scbox" class="contents">
3902 <div style="margin-left: 0em"><<span class="scTag">xs:complexType</span>
3903 <span class="scTag">name</span>="<span class="scContent">ProteinDomain</span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:simpleContent</span>><div style="margin-left: 1.5em"><<span class="scTag">xs:extension</span>
3904 <span class="scTag">base</span>="<span class="scContent">
3906 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
3907 </span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:attribute</span>
3908 <span class="scTag">name</span>="<span class="scContent">from</span>" <span class="scTag">type</span>="<span class="scContent">
3910 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:nonNegativeInteger</span>
3911 </span>" <span class="scTag">use</span>="<span class="scContent">required</span>"/></div>
3912 <div style="margin-left: 1.5em"><<span class="scTag">xs:attribute</span>
3913 <span class="scTag">name</span>="<span class="scContent">to</span>" <span class="scTag">type</span>="<span class="scContent">
3915 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:nonNegativeInteger</span>
3916 </span>" <span class="scTag">use</span>="<span class="scContent">required</span>"/></div>
3917 <div style="margin-left: 1.5em"><<span class="scTag">xs:attribute</span>
3918 <span class="scTag">name</span>="<span class="scContent">confidence</span>" <span class="scTag">type</span>="<span class="scContent">
3920 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:double</span>
3922 <div style="margin-left: 1.5em"><<span class="scTag">xs:attribute</span>
3923 <span class="scTag">name</span>="<span class="scContent">id</span>" <span class="scTag">type</span>="<span class="scContent">
3925 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
3926 </span>"/></div></<span class="scTag">xs:extension</span>></div></<span class="scTag">xs:simpleContent</span>></div></<span class="scTag">xs:complexType</span>></div>
3928 <script type="text/javascript">
3930 setState('h-1389097534_scbox', false);
3934 <div style="text-align: right; clear: both;">
3935 <a href="#top">top</a>
3938 <h3>Complex Type: <a name="h401516646" class="name">Reference</a>
3940 <table class="hierarchy">
3942 <th>Super-types:</th>
3950 <table class="properties">
3956 <th>Used by (from the same schema document)</th>
3957 <td>Complex Type <b>
3958 <a href="#h-1124608460">Clade</a>
3964 <a title="Look up 'Abstract' in glossary" href="phyloxml.xsd.html#term_Abstract">Abstract</a>
3969 <th>Documentation</th>
3970 <td class="documentation"> A literature reference for a clade. It is recommended to use the 'doi' attribute instead of
3971 the free text 'desc' element whenever possible. </td>
3974 <div class="sample box">
3976 <input type="button" id="h401516646_xibox_button" class="control"
3977 onclick="switchState('h401516646_xibox'); return false;"
3978 style="display: none"/>
3979 <span class="caption">XML Instance Representation</span>
3981 <div id="h401516646_xibox" class="contents">
3982 <div style="margin-left: 0em"><...<br/>
3983 <span style="margin-left: 0.5em"> doi="<span class="type">
3984 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Doi" type definition." href="#h-676028775">Doi</a>
3986 <span class="occurs">[0..1]</span>"</span>> <br/>
3987 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:desc> <span class="type">
3988 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:desc> <span class="occurs">[0..1]</span>
3989 </div></...></div>
3991 <script type="text/javascript">
3993 setState('h401516646_xibox', true);
3997 <div class="sample box">
3999 <input type="button" id="h401516646_diagram_button" class="control"
4000 onclick="switchState('h401516646_diagram'); return false;"
4001 style="display: none"/>
4002 <span class="caption">Diagram</span>
4004 <div id="h401516646_diagram" class="contents">
4005 <img usemap="#h1727164161" src="schemaDiagrams/h1727164161.png"/>
4007 Map ref: file:/D:/WORK/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester-atv/resources/phyloxml_schema/1.00//schemaDiagrams/h1727164161.map--><map name="h1727164161">
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4013 <script type="text/javascript">
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4019 <div class="schemaComponent box">
4021 <input type="button" id="h401516646_scbox_button" class="control"
4022 onclick="switchState('h401516646_scbox'); return false;"
4023 style="display: none"/>
4024 <span class="caption">Schema Component Representation</span>
4026 <div id="h401516646_scbox" class="contents">
4027 <div style="margin-left: 0em"><<span class="scTag">xs:complexType</span>
4028 <span class="scTag">name</span>="<span class="scContent">Reference</span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:sequence</span>><div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
4029 <span class="scTag">name</span>="<span class="scContent">desc</span>" <span class="scTag">type</span>="<span class="scContent">
4031 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
4032 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>"/></div></<span class="scTag">xs:sequence</span>></div>
4033 <div style="margin-left: 1.5em"><<span class="scTag">xs:attribute</span>
4034 <span class="scTag">name</span>="<span class="scContent">doi</span>" <span class="scTag">type</span>="<span class="scContent">
4036 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Doi" type definition." href="#h-676028775">Doi</a>
4038 </span>"/></div></<span class="scTag">xs:complexType</span>></div>
4040 <script type="text/javascript">
4042 setState('h401516646_scbox', false);
4046 <div style="text-align: right; clear: both;">
4047 <a href="#top">top</a>
4050 <h3>Complex Type: <a name="h-1794244794" class="name">Sequence</a>
4052 <table class="hierarchy">
4054 <th>Super-types:</th>
4062 <table class="properties">
4068 <th>Used by (from the same schema document)</th>
4069 <td>Complex Type <b>
4070 <a href="#h-1124608460">Clade</a>
4076 <a title="Look up 'Abstract' in glossary" href="phyloxml.xsd.html#term_Abstract">Abstract</a>
4081 <th>Documentation</th>
4082 <td class="documentation"> Element Sequence is used to represent a molecular sequence (Protein, DNA, RNA) associated
4083 with a node. 'symbol' is a short (maximal ten characters) symbol of the sequence (e.g. 'ACTM') whereas
4084 'name' is used for the full name (e.g. 'muscle Actin'). 'location' is used for the location of a sequence on
4085 a genome/chromosome. The actual sequence can be stored with the 'mol_seq' element. Attribute 'type' is used
4086 to indicate the type of sequence ('dna', 'rna', or 'aa'). One intended use for 'id_ref' is to link a
4087 sequence to a taxonomy (via the taxonomy's 'id_source') in case of multiple sequences and taxonomies per
4091 <div class="sample box">
4093 <input type="button" id="h-1794244794_xibox_button" class="control"
4094 onclick="switchState('h-1794244794_xibox'); return false;"
4095 style="display: none"/>
4096 <span class="caption">XML Instance Representation</span>
4098 <div id="h-1794244794_xibox" class="contents">
4099 <div style="margin-left: 0em"><...<br/>
4100 <span style="margin-left: 0.5em"> type="<span class="type">
4101 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "SequenceType" type definition." href="#h1408823200">SequenceType</a>
4103 <span class="occurs">[0..1]</span>"</span>
4105 <span style="margin-left: 0.5em"> id_source="<span class="type">
4106 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "id_source" type definition." href="#h-1482113798">id_source</a>
4108 <span class="occurs">[0..1]</span>"</span>
4110 <span style="margin-left: 0.5em"> id_ref="<span class="type">
4111 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "id_ref" type definition." href="#h577349652">id_ref</a>
4113 <span class="occurs">[0..1]</span>"</span>> <br/>
4114 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:symbol> <span class="type">
4115 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "SequenceSymbol" type definition." href="#h935679102">SequenceSymbol</a>
4116 </span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:symbol> <span class="occurs">[0..1]</span>
4118 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:accession> <span class="type">
4119 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Accession" type definition." href="#h-788356801">Accession</a>
4120 </span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:accession> <span class="occurs">[0..1]</span>
4122 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:name> <span class="type">
4123 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:name> <span class="occurs">[0..1]</span>
4125 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:location> <span class="type">
4126 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:location> <span class="occurs">[0..1]</span>
4128 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:mol_seq> <span class="type">
4129 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "MolSeq" type definition." href="#h-213750342">MolSeq</a>
4130 </span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:mol_seq> <span class="occurs">[0..1]</span>
4132 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:uri> <span class="type">
4133 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Uri" type definition." href="#h-676012345">Uri</a>
4134 </span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:uri> <span class="occurs">[0..1]</span>
4136 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:annotation> <span class="type">
4137 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Annotation" type definition." href="#h917087604">Annotation</a>
4138 </span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:annotation> <span class="occurs">[0..*]</span>
4140 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:domain_architecture> <span class="type">
4141 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "DomainArchitecture" type definition." href="#h259010940">DomainArchitecture</a>
4142 </span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:domain_architecture> <span class="occurs">[0..1]</span>
4144 <div class="other" style="margin-left: 1.5em">Allow any elements from a namespace other than this schema's namespace (lax validation). <span class="occurs">[0..*]</span>
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4158 <span class="caption">Diagram</span>
4160 <div id="h-1794244794_diagram" class="contents">
4161 <img usemap="#h1156064289" src="schemaDiagrams/h1156064289.png"/>
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4201 <input type="button" id="h-1794244794_scbox_button" class="control"
4202 onclick="switchState('h-1794244794_scbox'); return false;"
4203 style="display: none"/>
4204 <span class="caption">Schema Component Representation</span>
4206 <div id="h-1794244794_scbox" class="contents">
4207 <div style="margin-left: 0em"><<span class="scTag">xs:complexType</span>
4208 <span class="scTag">name</span>="<span class="scContent">Sequence</span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:sequence</span>><div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
4209 <span class="scTag">name</span>="<span class="scContent">symbol</span>" <span class="scTag">type</span>="<span class="scContent">
4211 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "SequenceSymbol" type definition." href="#h935679102">SequenceSymbol</a>
4213 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>"/></div>
4214 <div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
4215 <span class="scTag">name</span>="<span class="scContent">accession</span>" <span class="scTag">type</span>="<span class="scContent">
4217 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Accession" type definition." href="#h-788356801">Accession</a>
4219 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>"/></div>
4220 <div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
4221 <span class="scTag">name</span>="<span class="scContent">name</span>" <span class="scTag">type</span>="<span class="scContent">
4223 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
4224 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>"/></div>
4225 <div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
4226 <span class="scTag">name</span>="<span class="scContent">location</span>" <span class="scTag">type</span>="<span class="scContent">
4228 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
4229 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>"/></div>
4230 <div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
4231 <span class="scTag">name</span>="<span class="scContent">mol_seq</span>" <span class="scTag">type</span>="<span class="scContent">
4233 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "MolSeq" type definition." href="#h-213750342">MolSeq</a>
4235 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>"/></div>
4236 <div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
4237 <span class="scTag">name</span>="<span class="scContent">uri</span>" <span class="scTag">type</span>="<span class="scContent">
4239 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Uri" type definition." href="#h-676012345">Uri</a>
4241 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>"/></div>
4242 <div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
4243 <span class="scTag">name</span>="<span class="scContent">annotation</span>" <span class="scTag">type</span>="<span class="scContent">
4245 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Annotation" type definition." href="#h917087604">Annotation</a>
4247 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>" <span class="scTag">maxOccurs</span>="<span class="scContent">unbounded</span>"/></div>
4248 <div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
4249 <span class="scTag">name</span>="<span class="scContent">domain_architecture</span>" <span class="scTag">type</span>="<span class="scContent">
4251 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "DomainArchitecture" type definition." href="#h259010940">DomainArchitecture</a>
4253 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>"/></div>
4254 <div style="margin-left: 1.5em"><<span class="scTag">xs:any</span>
4255 <span class="scTag">minOccurs</span>="<span class="scContent">0</span>" <span class="scTag">maxOccurs</span>="<span class="scContent">unbounded</span>" <span class="scTag">processContents</span>="<span class="scContent">lax</span>" <span class="scTag">namespace</span>="<span class="scContent">##other</span>"/></div></<span class="scTag">xs:sequence</span>></div>
4256 <div style="margin-left: 1.5em"><<span class="scTag">xs:attribute</span>
4257 <span class="scTag">name</span>="<span class="scContent">type</span>" <span class="scTag">type</span>="<span class="scContent">
4259 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "SequenceType" type definition." href="#h1408823200">SequenceType</a>
4262 <div style="margin-left: 1.5em"><<span class="scTag">xs:attribute</span>
4263 <span class="scTag">name</span>="<span class="scContent">id_source</span>" <span class="scTag">type</span>="<span class="scContent">
4265 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "id_source" type definition." href="#h-1482113798">id_source</a>
4268 <div style="margin-left: 1.5em"><<span class="scTag">xs:attribute</span>
4269 <span class="scTag">name</span>="<span class="scContent">id_ref</span>" <span class="scTag">type</span>="<span class="scContent">
4271 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "id_ref" type definition." href="#h577349652">id_ref</a>
4273 </span>"/></div></<span class="scTag">xs:complexType</span>></div>
4275 <script type="text/javascript">
4277 setState('h-1794244794_scbox', false);
4281 <div style="text-align: right; clear: both;">
4282 <a href="#top">top</a>
4285 <h3>Complex Type: <a name="h-802965662" class="name">SequenceRelation</a>
4287 <table class="hierarchy">
4289 <th>Super-types:</th>
4297 <table class="properties">
4300 <td>SequenceRelation</td>
4303 <th>Used by (from the same schema document)</th>
4304 <td>Complex Type <b>
4305 <a href="#h535307528">Phylogeny</a>
4311 <a title="Look up 'Abstract' in glossary" href="phyloxml.xsd.html#term_Abstract">Abstract</a>
4316 <th>Documentation</th>
4317 <td class="documentation"> This is used to express a typed relationship between two sequences. For example it could be
4318 used to describe an orthology (in which case attribute 'type' is 'orthology'). </td>
4321 <div class="sample box">
4323 <input type="button" id="h-802965662_xibox_button" class="control"
4324 onclick="switchState('h-802965662_xibox'); return false;"
4325 style="display: none"/>
4326 <span class="caption">XML Instance Representation</span>
4328 <div id="h-802965662_xibox" class="contents">
4329 <div style="margin-left: 0em"><...<br/>
4330 <span style="margin-left: 0.5em"> id_ref_0="<span class="type">
4331 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "id_ref" type definition." href="#h577349652">id_ref</a>
4333 <span class="occurs">[1]</span>"</span>
4335 <span style="margin-left: 0.5em"> id_ref_1="<span class="type">
4336 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "id_ref" type definition." href="#h577349652">id_ref</a>
4338 <span class="occurs">[1]</span>"</span>
4340 <span style="margin-left: 0.5em"> distance="<span class="type">
4341 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:double</span>
4342 <span class="occurs">[0..1]</span>"</span>
4344 <span style="margin-left: 0.5em"> type="<span class="type">
4345 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "SequenceRelationType" type definition." href="#h519911868">SequenceRelationType</a>
4347 <span class="occurs">[1]</span>"</span>> <br/>
4348 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:confidence> <span class="type">
4349 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Confidence" type definition." href="#h-993584945">Confidence</a>
4350 </span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:confidence> <span class="occurs">[0..1]</span>
4351 </div></...></div>
4353 <script type="text/javascript">
4355 setState('h-802965662_xibox', true);
4359 <div class="sample box">
4361 <input type="button" id="h-802965662_diagram_button" class="control"
4362 onclick="switchState('h-802965662_diagram'); return false;"
4363 style="display: none"/>
4364 <span class="caption">Diagram</span>
4366 <div id="h-802965662_diagram" class="contents">
4367 <img usemap="#h230020485" src="schemaDiagrams/h230020485.png"/>
4369 Map ref: file:/D:/WORK/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester-atv/resources/phyloxml_schema/1.00//schemaDiagrams/h230020485.map--><map name="h230020485">
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4395 <span class="caption">Schema Component Representation</span>
4397 <div id="h-802965662_scbox" class="contents">
4398 <div style="margin-left: 0em"><<span class="scTag">xs:complexType</span>
4399 <span class="scTag">name</span>="<span class="scContent">SequenceRelation</span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:sequence</span>><div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
4400 <span class="scTag">name</span>="<span class="scContent">confidence</span>" <span class="scTag">type</span>="<span class="scContent">
4402 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Confidence" type definition." href="#h-993584945">Confidence</a>
4404 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>"/></div></<span class="scTag">xs:sequence</span>></div>
4405 <div style="margin-left: 1.5em"><<span class="scTag">xs:attribute</span>
4406 <span class="scTag">name</span>="<span class="scContent">id_ref_0</span>" <span class="scTag">type</span>="<span class="scContent">
4408 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "id_ref" type definition." href="#h577349652">id_ref</a>
4410 </span>" <span class="scTag">use</span>="<span class="scContent">required</span>"/></div>
4411 <div style="margin-left: 1.5em"><<span class="scTag">xs:attribute</span>
4412 <span class="scTag">name</span>="<span class="scContent">id_ref_1</span>" <span class="scTag">type</span>="<span class="scContent">
4414 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "id_ref" type definition." href="#h577349652">id_ref</a>
4416 </span>" <span class="scTag">use</span>="<span class="scContent">required</span>"/></div>
4417 <div style="margin-left: 1.5em"><<span class="scTag">xs:attribute</span>
4418 <span class="scTag">name</span>="<span class="scContent">distance</span>" <span class="scTag">type</span>="<span class="scContent">
4420 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:double</span>
4422 <div style="margin-left: 1.5em"><<span class="scTag">xs:attribute</span>
4423 <span class="scTag">name</span>="<span class="scContent">type</span>" <span class="scTag">type</span>="<span class="scContent">
4425 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "SequenceRelationType" type definition." href="#h519911868">SequenceRelationType</a>
4427 </span>" <span class="scTag">use</span>="<span class="scContent">required</span>"/></div></<span class="scTag">xs:complexType</span>></div>
4429 <script type="text/javascript">
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4435 <div style="text-align: right; clear: both;">
4436 <a href="#top">top</a>
4439 <h3>Complex Type: <a name="h888650454" class="name">Taxonomy</a>
4441 <table class="hierarchy">
4443 <th>Super-types:</th>
4451 <table class="properties">
4457 <th>Used by (from the same schema document)</th>
4458 <td>Complex Type <b>
4459 <a href="#h-1124608460">Clade</a>
4465 <a title="Look up 'Abstract' in glossary" href="phyloxml.xsd.html#term_Abstract">Abstract</a>
4470 <th>Documentation</th>
4471 <td class="documentation"> Element Taxonomy is used to describe taxonomic information for a clade. Element 'code' is
4472 intended to store UniProt/Swiss-Prot style organism codes (e.g. 'APLCA' for the California sea hare 'Aplysia
4473 californica'). Element 'id' is used for a unique identifier of a taxon (for example '6500' with
4474 'ncbi_taxonomy' as 'type' for the California sea hare). Attribute 'id_source' is used to link other elements
4475 to a taxonomy (on the xml-level).</td>
4478 <div class="sample box">
4480 <input type="button" id="h888650454_xibox_button" class="control"
4481 onclick="switchState('h888650454_xibox'); return false;"
4482 style="display: none"/>
4483 <span class="caption">XML Instance Representation</span>
4485 <div id="h888650454_xibox" class="contents">
4486 <div style="margin-left: 0em"><...<br/>
4487 <span style="margin-left: 0.5em"> type="<span class="type">
4488 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
4489 <span class="occurs">[0..1]</span>"</span>
4491 <span style="margin-left: 0.5em"> id_source="<span class="type">
4492 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "id_source" type definition." href="#h-1482113798">id_source</a>
4494 <span class="occurs">[0..1]</span>"</span>> <br/>
4495 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:id> <span class="type">
4496 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Id" type definition." href="#h-853091232">Id</a>
4497 </span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:id> <span class="occurs">[0..1]</span>
4499 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:code> <span class="type">
4500 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "TaxonomyCode" type definition." href="#h712147427">TaxonomyCode</a>
4501 </span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:code> <span class="occurs">[0..1]</span>
4503 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:scientific_name> <span class="type">
4504 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:scientific_name> <span class="occurs">[0..1]</span>
4506 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:common_name> <span class="type">
4507 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:common_name> <span class="occurs">[0..*]</span>
4509 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:rank> <span class="type">
4510 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Rank" type definition." href="#h518348337">Rank</a>
4511 </span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:rank> <span class="occurs">[0..1]</span>
4513 <div style="margin-left: 1.5em"><<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:uri> <span class="type">
4514 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Uri" type definition." href="#h-676012345">Uri</a>
4515 </span> </<a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:uri> <span class="occurs">[0..1]</span>
4517 <div class="other" style="margin-left: 1.5em">Allow any elements from a namespace other than this schema's namespace (lax validation). <span class="occurs">[0..*]</span>
4518 </div></...></div>
4520 <script type="text/javascript">
4522 setState('h888650454_xibox', true);
4526 <div class="sample box">
4528 <input type="button" id="h888650454_diagram_button" class="control"
4529 onclick="switchState('h888650454_diagram'); return false;"
4530 style="display: none"/>
4531 <span class="caption">Diagram</span>
4533 <div id="h888650454_diagram" class="contents">
4534 <img usemap="#h992625297" src="schemaDiagrams/h992625297.png"/>
4536 Map ref: file:/D:/WORK/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester-atv/resources/phyloxml_schema/1.00//schemaDiagrams/h992625297.map--><map name="h992625297">
4537 <area shape="rect" alt="h-853091232" coords="222,0,298,40"
4538 href="phyloxml.xsd.html#h-853091232"/>
4540 <area shape="rect" alt="h712147427" coords="222,50,306,90"
4541 href="phyloxml.xsd.html#h712147427"/>
4543 <area shape="rect" alt="h518348337" coords="222,200,306,240"
4544 href="phyloxml.xsd.html#h518348337"/>
4546 <area shape="rect" alt="h-676012345" coords="222,250,299,290"
4547 href="phyloxml.xsd.html#h-676012345"/>
4549 <area shape="rect" alt="h-1482113798" coords="136,387,273,413"
4550 href="phyloxml.xsd.html#h-1482113798"/>
4554 <script type="text/javascript">
4556 setState('h888650454_diagram', true);
4560 <div class="schemaComponent box">
4562 <input type="button" id="h888650454_scbox_button" class="control"
4563 onclick="switchState('h888650454_scbox'); return false;"
4564 style="display: none"/>
4565 <span class="caption">Schema Component Representation</span>
4567 <div id="h888650454_scbox" class="contents">
4568 <div style="margin-left: 0em"><<span class="scTag">xs:complexType</span>
4569 <span class="scTag">name</span>="<span class="scContent">Taxonomy</span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:sequence</span>><div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
4570 <span class="scTag">name</span>="<span class="scContent">id</span>" <span class="scTag">type</span>="<span class="scContent">
4572 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Id" type definition." href="#h-853091232">Id</a>
4574 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>"/></div>
4575 <div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
4576 <span class="scTag">name</span>="<span class="scContent">code</span>" <span class="scTag">type</span>="<span class="scContent">
4578 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "TaxonomyCode" type definition." href="#h712147427">TaxonomyCode</a>
4580 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>"/></div>
4581 <div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
4582 <span class="scTag">name</span>="<span class="scContent">scientific_name</span>" <span class="scTag">type</span>="<span class="scContent">
4584 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
4585 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>"/></div>
4586 <div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
4587 <span class="scTag">name</span>="<span class="scContent">common_name</span>" <span class="scTag">type</span>="<span class="scContent">
4589 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
4590 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>" <span class="scTag">maxOccurs</span>="<span class="scContent">unbounded</span>"/></div>
4591 <div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
4592 <span class="scTag">name</span>="<span class="scContent">rank</span>" <span class="scTag">type</span>="<span class="scContent">
4594 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Rank" type definition." href="#h518348337">Rank</a>
4596 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>"/></div>
4597 <div style="margin-left: 1.5em"><<span class="scTag">xs:element</span>
4598 <span class="scTag">name</span>="<span class="scContent">uri</span>" <span class="scTag">type</span>="<span class="scContent">
4600 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "Uri" type definition." href="#h-676012345">Uri</a>
4602 </span>" <span class="scTag">minOccurs</span>="<span class="scContent">0</span>"/></div>
4603 <div style="margin-left: 1.5em"><<span class="scTag">xs:any</span>
4604 <span class="scTag">minOccurs</span>="<span class="scContent">0</span>" <span class="scTag">maxOccurs</span>="<span class="scContent">unbounded</span>" <span class="scTag">processContents</span>="<span class="scContent">lax</span>" <span class="scTag">namespace</span>="<span class="scContent">##other</span>"/></div></<span class="scTag">xs:sequence</span>></div>
4605 <div style="margin-left: 1.5em"><<span class="scTag">xs:attribute</span>
4606 <span class="scTag">name</span>="<span class="scContent">type</span>" <span class="scTag">type</span>="<span class="scContent">
4608 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
4610 <div style="margin-left: 1.5em"><<span class="scTag">xs:attribute</span>
4611 <span class="scTag">name</span>="<span class="scContent">id_source</span>" <span class="scTag">type</span>="<span class="scContent">
4613 <a href="#ns_phy" title="Find out namespace of 'phy' prefix">phy</a>:<a title="Jump to "id_source" type definition." href="#h-1482113798">id_source</a>
4615 </span>"/></div></<span class="scTag">xs:complexType</span>></div>
4617 <script type="text/javascript">
4619 setState('h888650454_scbox', false);
4623 <div style="text-align: right; clear: both;">
4624 <a href="#top">top</a>
4627 <h3>Complex Type: <a name="h-676012345" class="name">Uri</a>
4629 <table class="hierarchy">
4631 <th>Super-types:</th>
4634 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:anyURI</span> < <strong>Uri</strong> (by extension)</td>
4641 <table class="properties">
4647 <th>Used by (from the same schema document)</th>
4648 <td>Complex Type <b>
4649 <a href="#h888650454">Taxonomy</a>
4650 </b>, Complex Type <b>
4651 <a href="#h-1794244794">Sequence</a>
4652 </b>, Complex Type <b>
4653 <a href="#h917087604">Annotation</a>
4659 <a title="Look up 'Abstract' in glossary" href="phyloxml.xsd.html#term_Abstract">Abstract</a>
4664 <th>Documentation</th>
4665 <td class="documentation"> A uniform resource identifier. In general, this is expected to be an URL (for example, to
4666 link to an image on a website, in which case the 'type' attribute might be 'image' and 'desc' might be
4667 'image of a California sea hare'). </td>
4670 <div class="sample box">
4672 <input type="button" id="h-676012345_xibox_button" class="control"
4673 onclick="switchState('h-676012345_xibox'); return false;"
4674 style="display: none"/>
4675 <span class="caption">XML Instance Representation</span>
4677 <div id="h-676012345_xibox" class="contents">
4678 <div style="margin-left: 0em"><...<br/>
4679 <span style="margin-left: 0.5em" class="newFields"> desc="<span class="type">
4680 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
4681 <span class="occurs">[0..1]</span>"</span>
4683 <span style="margin-left: 0.5em" class="newFields"> type="<span class="type">
4684 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
4685 <span class="occurs">[0..1]</span>"</span>> <br/>
4686 <span style="margin-left: 1.5em">
4688 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:anyURI</span>
4690 <br/></...></div>
4692 <script type="text/javascript">
4694 setState('h-676012345_xibox', true);
4698 <div class="sample box">
4700 <input type="button" id="h-676012345_diagram_button" class="control"
4701 onclick="switchState('h-676012345_diagram'); return false;"
4702 style="display: none"/>
4703 <span class="caption">Diagram</span>
4705 <div id="h-676012345_diagram" class="contents">
4706 <img usemap="#h-1930055872" src="schemaDiagrams/h-1930055872.png"/>
4708 Map ref: file:/D:/WORK/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester-atv/resources/phyloxml_schema/1.00//schemaDiagrams/h-1930055872.map--><map name="h-1930055872">
4711 <script type="text/javascript">
4713 setState('h-676012345_diagram', true);
4717 <div class="schemaComponent box">
4719 <input type="button" id="h-676012345_scbox_button" class="control"
4720 onclick="switchState('h-676012345_scbox'); return false;"
4721 style="display: none"/>
4722 <span class="caption">Schema Component Representation</span>
4724 <div id="h-676012345_scbox" class="contents">
4725 <div style="margin-left: 0em"><<span class="scTag">xs:complexType</span>
4726 <span class="scTag">name</span>="<span class="scContent">Uri</span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:simpleContent</span>><div style="margin-left: 1.5em"><<span class="scTag">xs:extension</span>
4727 <span class="scTag">base</span>="<span class="scContent">
4729 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:anyURI</span>
4730 </span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:attribute</span>
4731 <span class="scTag">name</span>="<span class="scContent">desc</span>" <span class="scTag">type</span>="<span class="scContent">
4733 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
4735 <div style="margin-left: 1.5em"><<span class="scTag">xs:attribute</span>
4736 <span class="scTag">name</span>="<span class="scContent">type</span>" <span class="scTag">type</span>="<span class="scContent">
4738 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
4739 </span>"/></div></<span class="scTag">xs:extension</span>></div></<span class="scTag">xs:simpleContent</span>></div></<span class="scTag">xs:complexType</span>></div>
4741 <script type="text/javascript">
4743 setState('h-676012345_scbox', false);
4747 <div style="text-align: right; clear: both;">
4748 <a href="#top">top</a>
4751 <h3>Simple Type: <a name="h-763252414" class="name">AppliesTo</a>
4753 <table class="hierarchy">
4755 <th>Super-types:</th>
4758 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span> < <strong>AppliesTo</strong> (by restriction)</td>
4765 <table class="properties">
4771 <th>Used by (from the same schema document)</th>
4772 <td>Complex Type <b>
4773 <a href="#h158033242">Property</a>
4781 <li>Base XSD Type: token</li>
4785 <em>value</em> comes from list: {'phylogeny'|'clade'|'node'|'annotation'|'parent_branch'|'other'}</li>
4790 <div class="sample box">
4792 <input type="button" id="h-763252414_diagram_button" class="control"
4793 onclick="switchState('h-763252414_diagram'); return false;"
4794 style="display: none"/>
4795 <span class="caption">Diagram</span>
4797 <div id="h-763252414_diagram" class="contents">
4798 <img usemap="#h-553597019" src="schemaDiagrams/h-553597019.png"/>
4800 Map ref: file:/D:/WORK/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester-atv/resources/phyloxml_schema/1.00//schemaDiagrams/h-553597019.map--><map name="h-553597019">
4803 <script type="text/javascript">
4805 setState('h-763252414_diagram', true);
4809 <div class="schemaComponent box">
4811 <input type="button" id="h-763252414_scbox_button" class="control"
4812 onclick="switchState('h-763252414_scbox'); return false;"
4813 style="display: none"/>
4814 <span class="caption">Schema Component Representation</span>
4816 <div id="h-763252414_scbox" class="contents">
4817 <div style="margin-left: 0em"><<span class="scTag">xs:simpleType</span>
4818 <span class="scTag">name</span>="<span class="scContent">AppliesTo</span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:restriction</span>
4819 <span class="scTag">base</span>="<span class="scContent">
4821 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
4822 </span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
4823 <span class="scTag">value</span>="<span class="scContent">phylogeny</span>"/></div>
4824 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
4825 <span class="scTag">value</span>="<span class="scContent">clade</span>"/></div>
4826 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
4827 <span class="scTag">value</span>="<span class="scContent">node</span>"/></div>
4828 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
4829 <span class="scTag">value</span>="<span class="scContent">annotation</span>"/></div>
4830 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
4831 <span class="scTag">value</span>="<span class="scContent">parent_branch</span>"/></div>
4832 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
4833 <span class="scTag">value</span>="<span class="scContent">other</span>"/></div></<span class="scTag">xs:restriction</span>></div></<span class="scTag">xs:simpleType</span>></div>
4835 <script type="text/javascript">
4837 setState('h-763252414_scbox', false);
4841 <div style="text-align: right; clear: both;">
4842 <a href="#top">top</a>
4845 <h3>Simple Type: <a name="h-676028775" class="name">Doi</a>
4847 <table class="hierarchy">
4849 <th>Super-types:</th>
4852 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span> < <strong>Doi</strong> (by restriction)</td>
4859 <table class="properties">
4865 <th>Used by (from the same schema document)</th>
4866 <td>Complex Type <b>
4867 <a href="#h401516646">Reference</a>
4875 <li>Base XSD Type: token</li>
4879 <em>pattern</em> = [a-zA-Z0-9_\.]+/[a-zA-Z0-9_\.]+</li>
4884 <div class="sample box">
4886 <input type="button" id="h-676028775_diagram_button" class="control"
4887 onclick="switchState('h-676028775_diagram'); return false;"
4888 style="display: none"/>
4889 <span class="caption">Diagram</span>
4891 <div id="h-676028775_diagram" class="contents">
4892 <img usemap="#h-230267218" src="schemaDiagrams/h-230267218.png"/>
4894 Map ref: file:/D:/WORK/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester-atv/resources/phyloxml_schema/1.00//schemaDiagrams/h-230267218.map--><map name="h-230267218">
4897 <script type="text/javascript">
4899 setState('h-676028775_diagram', true);
4903 <div class="schemaComponent box">
4905 <input type="button" id="h-676028775_scbox_button" class="control"
4906 onclick="switchState('h-676028775_scbox'); return false;"
4907 style="display: none"/>
4908 <span class="caption">Schema Component Representation</span>
4910 <div id="h-676028775_scbox" class="contents">
4911 <div style="margin-left: 0em"><<span class="scTag">xs:simpleType</span>
4912 <span class="scTag">name</span>="<span class="scContent">Doi</span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:restriction</span>
4913 <span class="scTag">base</span>="<span class="scContent">
4915 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
4916 </span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:pattern</span>
4917 <span class="scTag">value</span>="<span class="scContent">[a-zA-Z0-9_\.]+/[a-zA-Z0-9_\.]+</span>"/></div></<span class="scTag">xs:restriction</span>></div></<span class="scTag">xs:simpleType</span>></div>
4919 <script type="text/javascript">
4921 setState('h-676028775_scbox', false);
4925 <div style="text-align: right; clear: both;">
4926 <a href="#top">top</a>
4929 <h3>Simple Type: <a name="h1358103055" class="name">EventType</a>
4931 <table class="hierarchy">
4933 <th>Super-types:</th>
4936 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span> < <strong>EventType</strong> (by restriction)</td>
4943 <table class="properties">
4949 <th>Used by (from the same schema document)</th>
4950 <td>Complex Type <b>
4951 <a href="#h-436501026">Events</a>
4959 <li>Base XSD Type: token</li>
4963 <em>value</em> comes from list: {'transfer'|'fusion'|'speciation_or_duplication'|'other'|'mixed'|'unassigned'}</li>
4968 <div class="sample box">
4970 <input type="button" id="h1358103055_diagram_button" class="control"
4971 onclick="switchState('h1358103055_diagram'); return false;"
4972 style="display: none"/>
4973 <span class="caption">Diagram</span>
4975 <div id="h1358103055_diagram" class="contents">
4976 <img usemap="#h77064440" src="schemaDiagrams/h77064440.png"/>
4978 Map ref: file:/D:/WORK/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester-atv/resources/phyloxml_schema/1.00//schemaDiagrams/h77064440.map--><map name="h77064440">
4981 <script type="text/javascript">
4983 setState('h1358103055_diagram', true);
4987 <div class="schemaComponent box">
4989 <input type="button" id="h1358103055_scbox_button" class="control"
4990 onclick="switchState('h1358103055_scbox'); return false;"
4991 style="display: none"/>
4992 <span class="caption">Schema Component Representation</span>
4994 <div id="h1358103055_scbox" class="contents">
4995 <div style="margin-left: 0em"><<span class="scTag">xs:simpleType</span>
4996 <span class="scTag">name</span>="<span class="scContent">EventType</span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:restriction</span>
4997 <span class="scTag">base</span>="<span class="scContent">
4999 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
5000 </span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5001 <span class="scTag">value</span>="<span class="scContent">transfer</span>"/></div>
5002 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5003 <span class="scTag">value</span>="<span class="scContent">fusion</span>"/></div>
5004 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5005 <span class="scTag">value</span>="<span class="scContent">speciation_or_duplication</span>"/></div>
5006 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5007 <span class="scTag">value</span>="<span class="scContent">other</span>"/></div>
5008 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5009 <span class="scTag">value</span>="<span class="scContent">mixed</span>"/></div>
5010 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5011 <span class="scTag">value</span>="<span class="scContent">unassigned</span>"/></div></<span class="scTag">xs:restriction</span>></div></<span class="scTag">xs:simpleType</span>></div>
5013 <script type="text/javascript">
5015 setState('h1358103055_scbox', false);
5019 <div style="text-align: right; clear: both;">
5020 <a href="#top">top</a>
5023 <h3>Simple Type: <a name="h-213750342" class="name">MolSeq</a>
5025 <table class="hierarchy">
5027 <th>Super-types:</th>
5030 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span> < <strong>MolSeq</strong> (by restriction)</td>
5037 <table class="properties">
5043 <th>Used by (from the same schema document)</th>
5044 <td>Complex Type <b>
5045 <a href="#h-1794244794">Sequence</a>
5053 <li>Base XSD Type: token</li>
5057 <em>pattern</em> = [a-zA-Z\.\-\?\*_]+</li>
5062 <div class="sample box">
5064 <input type="button" id="h-213750342_diagram_button" class="control"
5065 onclick="switchState('h-213750342_diagram'); return false;"
5066 style="display: none"/>
5067 <span class="caption">Diagram</span>
5069 <div id="h-213750342_diagram" class="contents">
5070 <img usemap="#h-100858323" src="schemaDiagrams/h-100858323.png"/>
5072 Map ref: file:/D:/WORK/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester-atv/resources/phyloxml_schema/1.00//schemaDiagrams/h-100858323.map--><map name="h-100858323">
5075 <script type="text/javascript">
5077 setState('h-213750342_diagram', true);
5081 <div class="schemaComponent box">
5083 <input type="button" id="h-213750342_scbox_button" class="control"
5084 onclick="switchState('h-213750342_scbox'); return false;"
5085 style="display: none"/>
5086 <span class="caption">Schema Component Representation</span>
5088 <div id="h-213750342_scbox" class="contents">
5089 <div style="margin-left: 0em"><<span class="scTag">xs:simpleType</span>
5090 <span class="scTag">name</span>="<span class="scContent">MolSeq</span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:restriction</span>
5091 <span class="scTag">base</span>="<span class="scContent">
5093 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
5094 </span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:pattern</span>
5095 <span class="scTag">value</span>="<span class="scContent">[a-zA-Z\.\-\?\*_]+</span>"/></div></<span class="scTag">xs:restriction</span>></div></<span class="scTag">xs:simpleType</span>></div>
5097 <script type="text/javascript">
5099 setState('h-213750342_scbox', false);
5103 <div style="text-align: right; clear: both;">
5104 <a href="#top">top</a>
5107 <h3>Simple Type: <a name="h-54338178" class="name">PropertyDataType</a>
5109 <table class="hierarchy">
5111 <th>Super-types:</th>
5114 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span> < <strong>PropertyDataType</strong> (by restriction)</td>
5121 <table class="properties">
5124 <td>PropertyDataType</td>
5127 <th>Used by (from the same schema document)</th>
5128 <td>Complex Type <b>
5129 <a href="#h158033242">Property</a>
5137 <li>Base XSD Type: token</li>
5141 <em>value</em> comes from list: {'xsd:string'|'xsd:boolean'|'xsd:decimal'|'xsd:float'|'xsd:double'|'xsd:duration'|'xsd:dateTime'|'xsd:time'|'xsd:date'|'xsd:gYearMonth'|'xsd:gYear'|'xsd:gMonthDay'|'xsd:gDay'|'xsd:gMonth'|'xsd:hexBinary'|'xsd:base64Binary'|'xsd:anyURI'|'xsd:normalizedString'|'xsd:token'|'xsd:integer'|'xsd:nonPositiveInteger'|'xsd:negativeInteger'|'xsd:long'|'xsd:int'|'xsd:short'|'xsd:byte'|'xsd:nonNegativeInteger'|'xsd:unsignedLong'|'xsd:unsignedInt'|'xsd:unsignedShort'|'xsd:unsignedByte'|'xsd:positiveInteger'}</li>
5146 <div class="sample box">
5148 <input type="button" id="h-54338178_diagram_button" class="control"
5149 onclick="switchState('h-54338178_diagram'); return false;"
5150 style="display: none"/>
5151 <span class="caption">Diagram</span>
5153 <div id="h-54338178_diagram" class="contents">
5154 <img usemap="#h-624240407" src="schemaDiagrams/h-624240407.png"/>
5156 Map ref: file:/D:/WORK/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester-atv/resources/phyloxml_schema/1.00//schemaDiagrams/h-624240407.map--><map name="h-624240407">
5159 <script type="text/javascript">
5161 setState('h-54338178_diagram', true);
5165 <div class="schemaComponent box">
5167 <input type="button" id="h-54338178_scbox_button" class="control"
5168 onclick="switchState('h-54338178_scbox'); return false;"
5169 style="display: none"/>
5170 <span class="caption">Schema Component Representation</span>
5172 <div id="h-54338178_scbox" class="contents">
5173 <div style="margin-left: 0em"><<span class="scTag">xs:simpleType</span>
5174 <span class="scTag">name</span>="<span class="scContent">PropertyDataType</span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:restriction</span>
5175 <span class="scTag">base</span>="<span class="scContent">
5177 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
5178 </span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5179 <span class="scTag">value</span>="<span class="scContent">xsd:string</span>"/></div>
5180 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5181 <span class="scTag">value</span>="<span class="scContent">xsd:boolean</span>"/></div>
5182 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5183 <span class="scTag">value</span>="<span class="scContent">xsd:decimal</span>"/></div>
5184 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5185 <span class="scTag">value</span>="<span class="scContent">xsd:float</span>"/></div>
5186 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5187 <span class="scTag">value</span>="<span class="scContent">xsd:double</span>"/></div>
5188 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5189 <span class="scTag">value</span>="<span class="scContent">xsd:duration</span>"/></div>
5190 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5191 <span class="scTag">value</span>="<span class="scContent">xsd:dateTime</span>"/></div>
5192 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5193 <span class="scTag">value</span>="<span class="scContent">xsd:time</span>"/></div>
5194 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5195 <span class="scTag">value</span>="<span class="scContent">xsd:date</span>"/></div>
5196 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5197 <span class="scTag">value</span>="<span class="scContent">xsd:gYearMonth</span>"/></div>
5198 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5199 <span class="scTag">value</span>="<span class="scContent">xsd:gYear</span>"/></div>
5200 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5201 <span class="scTag">value</span>="<span class="scContent">xsd:gMonthDay</span>"/></div>
5202 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5203 <span class="scTag">value</span>="<span class="scContent">xsd:gDay</span>"/></div>
5204 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5205 <span class="scTag">value</span>="<span class="scContent">xsd:gMonth</span>"/></div>
5206 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5207 <span class="scTag">value</span>="<span class="scContent">xsd:hexBinary</span>"/></div>
5208 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5209 <span class="scTag">value</span>="<span class="scContent">xsd:base64Binary</span>"/></div>
5210 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5211 <span class="scTag">value</span>="<span class="scContent">xsd:anyURI</span>"/></div>
5212 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5213 <span class="scTag">value</span>="<span class="scContent">xsd:normalizedString</span>"/></div>
5214 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5215 <span class="scTag">value</span>="<span class="scContent">xsd:token</span>"/></div>
5216 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5217 <span class="scTag">value</span>="<span class="scContent">xsd:integer</span>"/></div>
5218 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5219 <span class="scTag">value</span>="<span class="scContent">xsd:nonPositiveInteger</span>"/></div>
5220 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5221 <span class="scTag">value</span>="<span class="scContent">xsd:negativeInteger</span>"/></div>
5222 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5223 <span class="scTag">value</span>="<span class="scContent">xsd:long</span>"/></div>
5224 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5225 <span class="scTag">value</span>="<span class="scContent">xsd:int</span>"/></div>
5226 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5227 <span class="scTag">value</span>="<span class="scContent">xsd:short</span>"/></div>
5228 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5229 <span class="scTag">value</span>="<span class="scContent">xsd:byte</span>"/></div>
5230 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5231 <span class="scTag">value</span>="<span class="scContent">xsd:nonNegativeInteger</span>"/></div>
5232 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5233 <span class="scTag">value</span>="<span class="scContent">xsd:unsignedLong</span>"/></div>
5234 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5235 <span class="scTag">value</span>="<span class="scContent">xsd:unsignedInt</span>"/></div>
5236 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5237 <span class="scTag">value</span>="<span class="scContent">xsd:unsignedShort</span>"/></div>
5238 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5239 <span class="scTag">value</span>="<span class="scContent">xsd:unsignedByte</span>"/></div>
5240 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5241 <span class="scTag">value</span>="<span class="scContent">xsd:positiveInteger</span>"/></div></<span class="scTag">xs:restriction</span>></div></<span class="scTag">xs:simpleType</span>></div>
5243 <script type="text/javascript">
5245 setState('h-54338178_scbox', false);
5249 <div style="text-align: right; clear: both;">
5250 <a href="#top">top</a>
5253 <h3>Simple Type: <a name="h518348337" class="name">Rank</a>
5255 <table class="hierarchy">
5257 <th>Super-types:</th>
5260 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span> < <strong>Rank</strong> (by restriction)</td>
5267 <table class="properties">
5273 <th>Used by (from the same schema document)</th>
5274 <td>Complex Type <b>
5275 <a href="#h888650454">Taxonomy</a>
5283 <li>Base XSD Type: token</li>
5287 <em>value</em> comes from list: {'domain'|'kingdom'|'subkingdom'|'branch'|'infrakingdom'|'superphylum'|'phylum'|'subphylum'|'infraphylum'|'microphylum'|'superdivision'|'division'|'subdivision'|'infradivision'|'superclass'|'class'|'subclass'|'infraclass'|'superlegion'|'legion'|'sublegion'|'infralegion'|'supercohort'|'cohort'|'subcohort'|'infracohort'|'superorder'|'order'|'suborder'|'superfamily'|'family'|'subfamily'|'supertribe'|'tribe'|'subtribe'|'infratribe'|'genus'|'subgenus'|'superspecies'|'species'|'subspecies'|'variety'|'subvariety'|'form'|'subform'|'cultivar'|'unknown'|'other'}</li>
5292 <div class="sample box">
5294 <input type="button" id="h518348337_diagram_button" class="control"
5295 onclick="switchState('h518348337_diagram'); return false;"
5296 style="display: none"/>
5297 <span class="caption">Diagram</span>
5299 <div id="h518348337_diagram" class="contents">
5300 <img usemap="#h-1363552746" src="schemaDiagrams/h-1363552746.png"/>
5302 Map ref: file:/D:/WORK/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester-atv/resources/phyloxml_schema/1.00//schemaDiagrams/h-1363552746.map--><map name="h-1363552746">
5305 <script type="text/javascript">
5307 setState('h518348337_diagram', true);
5311 <div class="schemaComponent box">
5313 <input type="button" id="h518348337_scbox_button" class="control"
5314 onclick="switchState('h518348337_scbox'); return false;"
5315 style="display: none"/>
5316 <span class="caption">Schema Component Representation</span>
5318 <div id="h518348337_scbox" class="contents">
5319 <div style="margin-left: 0em"><<span class="scTag">xs:simpleType</span>
5320 <span class="scTag">name</span>="<span class="scContent">Rank</span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:restriction</span>
5321 <span class="scTag">base</span>="<span class="scContent">
5323 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
5324 </span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5325 <span class="scTag">value</span>="<span class="scContent">domain</span>"/></div>
5326 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5327 <span class="scTag">value</span>="<span class="scContent">kingdom</span>"/></div>
5328 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5329 <span class="scTag">value</span>="<span class="scContent">subkingdom</span>"/></div>
5330 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5331 <span class="scTag">value</span>="<span class="scContent">branch</span>"/></div>
5332 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5333 <span class="scTag">value</span>="<span class="scContent">infrakingdom</span>"/></div>
5334 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5335 <span class="scTag">value</span>="<span class="scContent">superphylum</span>"/></div>
5336 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5337 <span class="scTag">value</span>="<span class="scContent">phylum</span>"/></div>
5338 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5339 <span class="scTag">value</span>="<span class="scContent">subphylum</span>"/></div>
5340 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5341 <span class="scTag">value</span>="<span class="scContent">infraphylum</span>"/></div>
5342 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5343 <span class="scTag">value</span>="<span class="scContent">microphylum</span>"/></div>
5344 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5345 <span class="scTag">value</span>="<span class="scContent">superdivision</span>"/></div>
5346 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5347 <span class="scTag">value</span>="<span class="scContent">division</span>"/></div>
5348 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5349 <span class="scTag">value</span>="<span class="scContent">subdivision</span>"/></div>
5350 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5351 <span class="scTag">value</span>="<span class="scContent">infradivision</span>"/></div>
5352 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5353 <span class="scTag">value</span>="<span class="scContent">superclass</span>"/></div>
5354 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5355 <span class="scTag">value</span>="<span class="scContent">class</span>"/></div>
5356 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5357 <span class="scTag">value</span>="<span class="scContent">subclass</span>"/></div>
5358 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5359 <span class="scTag">value</span>="<span class="scContent">infraclass</span>"/></div>
5360 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5361 <span class="scTag">value</span>="<span class="scContent">superlegion</span>"/></div>
5362 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5363 <span class="scTag">value</span>="<span class="scContent">legion</span>"/></div>
5364 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5365 <span class="scTag">value</span>="<span class="scContent">sublegion</span>"/></div>
5366 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5367 <span class="scTag">value</span>="<span class="scContent">infralegion</span>"/></div>
5368 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5369 <span class="scTag">value</span>="<span class="scContent">supercohort</span>"/></div>
5370 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5371 <span class="scTag">value</span>="<span class="scContent">cohort</span>"/></div>
5372 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5373 <span class="scTag">value</span>="<span class="scContent">subcohort</span>"/></div>
5374 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5375 <span class="scTag">value</span>="<span class="scContent">infracohort</span>"/></div>
5376 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5377 <span class="scTag">value</span>="<span class="scContent">superorder</span>"/></div>
5378 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5379 <span class="scTag">value</span>="<span class="scContent">order</span>"/></div>
5380 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5381 <span class="scTag">value</span>="<span class="scContent">suborder</span>"/></div>
5382 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5383 <span class="scTag">value</span>="<span class="scContent">superfamily</span>"/></div>
5384 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5385 <span class="scTag">value</span>="<span class="scContent">family</span>"/></div>
5386 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5387 <span class="scTag">value</span>="<span class="scContent">subfamily</span>"/></div>
5388 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5389 <span class="scTag">value</span>="<span class="scContent">supertribe</span>"/></div>
5390 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5391 <span class="scTag">value</span>="<span class="scContent">tribe</span>"/></div>
5392 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5393 <span class="scTag">value</span>="<span class="scContent">subtribe</span>"/></div>
5394 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5395 <span class="scTag">value</span>="<span class="scContent">infratribe</span>"/></div>
5396 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5397 <span class="scTag">value</span>="<span class="scContent">genus</span>"/></div>
5398 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5399 <span class="scTag">value</span>="<span class="scContent">subgenus</span>"/></div>
5400 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5401 <span class="scTag">value</span>="<span class="scContent">superspecies</span>"/></div>
5402 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5403 <span class="scTag">value</span>="<span class="scContent">species</span>"/></div>
5404 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5405 <span class="scTag">value</span>="<span class="scContent">subspecies</span>"/></div>
5406 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5407 <span class="scTag">value</span>="<span class="scContent">variety</span>"/></div>
5408 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5409 <span class="scTag">value</span>="<span class="scContent">subvariety</span>"/></div>
5410 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5411 <span class="scTag">value</span>="<span class="scContent">form</span>"/></div>
5412 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5413 <span class="scTag">value</span>="<span class="scContent">subform</span>"/></div>
5414 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5415 <span class="scTag">value</span>="<span class="scContent">cultivar</span>"/></div>
5416 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5417 <span class="scTag">value</span>="<span class="scContent">unknown</span>"/></div>
5418 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5419 <span class="scTag">value</span>="<span class="scContent">other</span>"/></div></<span class="scTag">xs:restriction</span>></div></<span class="scTag">xs:simpleType</span>></div>
5421 <script type="text/javascript">
5423 setState('h518348337_scbox', false);
5427 <div style="text-align: right; clear: both;">
5428 <a href="#top">top</a>
5431 <h3>Simple Type: <a name="h519911868" class="name">SequenceRelationType</a>
5433 <table class="hierarchy">
5435 <th>Super-types:</th>
5438 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span> < <strong>SequenceRelationType</strong> (by restriction)</td>
5445 <table class="properties">
5448 <td>SequenceRelationType</td>
5451 <th>Used by (from the same schema document)</th>
5452 <td>Complex Type <b>
5453 <a href="#h-802965662">SequenceRelation</a>
5461 <li>Base XSD Type: token</li>
5465 <em>value</em> comes from list: {'orthology'|'one_to_one_orthology'|'super_orthology'|'paralogy'|'ultra_paralogy'|'xenology'|'unknown'|'other'}</li>
5470 <div class="sample box">
5472 <input type="button" id="h519911868_diagram_button" class="control"
5473 onclick="switchState('h519911868_diagram'); return false;"
5474 style="display: none"/>
5475 <span class="caption">Diagram</span>
5477 <div id="h519911868_diagram" class="contents">
5478 <img usemap="#h-465227925" src="schemaDiagrams/h-465227925.png"/>
5480 Map ref: file:/D:/WORK/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester-atv/resources/phyloxml_schema/1.00//schemaDiagrams/h-465227925.map--><map name="h-465227925">
5483 <script type="text/javascript">
5485 setState('h519911868_diagram', true);
5489 <div class="schemaComponent box">
5491 <input type="button" id="h519911868_scbox_button" class="control"
5492 onclick="switchState('h519911868_scbox'); return false;"
5493 style="display: none"/>
5494 <span class="caption">Schema Component Representation</span>
5496 <div id="h519911868_scbox" class="contents">
5497 <div style="margin-left: 0em"><<span class="scTag">xs:simpleType</span>
5498 <span class="scTag">name</span>="<span class="scContent">SequenceRelationType</span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:restriction</span>
5499 <span class="scTag">base</span>="<span class="scContent">
5501 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
5502 </span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5503 <span class="scTag">value</span>="<span class="scContent">orthology</span>"/></div>
5504 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5505 <span class="scTag">value</span>="<span class="scContent">one_to_one_orthology</span>"/></div>
5506 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5507 <span class="scTag">value</span>="<span class="scContent">super_orthology</span>"/></div>
5508 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5509 <span class="scTag">value</span>="<span class="scContent">paralogy</span>"/></div>
5510 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5511 <span class="scTag">value</span>="<span class="scContent">ultra_paralogy</span>"/></div>
5512 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5513 <span class="scTag">value</span>="<span class="scContent">xenology</span>"/></div>
5514 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5515 <span class="scTag">value</span>="<span class="scContent">unknown</span>"/></div>
5516 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5517 <span class="scTag">value</span>="<span class="scContent">other</span>"/></div></<span class="scTag">xs:restriction</span>></div></<span class="scTag">xs:simpleType</span>></div>
5519 <script type="text/javascript">
5521 setState('h519911868_scbox', false);
5525 <div style="text-align: right; clear: both;">
5526 <a href="#top">top</a>
5529 <h3>Simple Type: <a name="h935679102" class="name">SequenceSymbol</a>
5531 <table class="hierarchy">
5533 <th>Super-types:</th>
5536 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span> < <strong>SequenceSymbol</strong> (by restriction)</td>
5543 <table class="properties">
5546 <td>SequenceSymbol</td>
5549 <th>Used by (from the same schema document)</th>
5550 <td>Complex Type <b>
5551 <a href="#h-1794244794">Sequence</a>
5559 <li>Base XSD Type: token</li>
5563 <em>pattern</em> = \S{1,10}</li>
5568 <div class="sample box">
5570 <input type="button" id="h935679102_diagram_button" class="control"
5571 onclick="switchState('h935679102_diagram'); return false;"
5572 style="display: none"/>
5573 <span class="caption">Diagram</span>
5575 <div id="h935679102_diagram" class="contents">
5576 <img usemap="#h516473321" src="schemaDiagrams/h516473321.png"/>
5578 Map ref: file:/D:/WORK/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester-atv/resources/phyloxml_schema/1.00//schemaDiagrams/h516473321.map--><map name="h516473321">
5581 <script type="text/javascript">
5583 setState('h935679102_diagram', true);
5587 <div class="schemaComponent box">
5589 <input type="button" id="h935679102_scbox_button" class="control"
5590 onclick="switchState('h935679102_scbox'); return false;"
5591 style="display: none"/>
5592 <span class="caption">Schema Component Representation</span>
5594 <div id="h935679102_scbox" class="contents">
5595 <div style="margin-left: 0em"><<span class="scTag">xs:simpleType</span>
5596 <span class="scTag">name</span>="<span class="scContent">SequenceSymbol</span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:restriction</span>
5597 <span class="scTag">base</span>="<span class="scContent">
5599 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
5600 </span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:pattern</span>
5601 <span class="scTag">value</span>="<span class="scContent">\S{1,10}</span>"/></div></<span class="scTag">xs:restriction</span>></div></<span class="scTag">xs:simpleType</span>></div>
5603 <script type="text/javascript">
5605 setState('h935679102_scbox', false);
5609 <div style="text-align: right; clear: both;">
5610 <a href="#top">top</a>
5613 <h3>Simple Type: <a name="h1408823200" class="name">SequenceType</a>
5615 <table class="hierarchy">
5617 <th>Super-types:</th>
5620 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span> < <strong>SequenceType</strong> (by restriction)</td>
5627 <table class="properties">
5630 <td>SequenceType</td>
5633 <th>Used by (from the same schema document)</th>
5634 <td>Complex Type <b>
5635 <a href="#h-1794244794">Sequence</a>
5643 <li>Base XSD Type: token</li>
5647 <em>value</em> comes from list: {'rna'|'dna'|'aa'}</li>
5652 <div class="sample box">
5654 <input type="button" id="h1408823200_diagram_button" class="control"
5655 onclick="switchState('h1408823200_diagram'); return false;"
5656 style="display: none"/>
5657 <span class="caption">Diagram</span>
5659 <div id="h1408823200_diagram" class="contents">
5660 <img usemap="#h-2043228153" src="schemaDiagrams/h-2043228153.png"/>
5662 Map ref: file:/D:/WORK/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester-atv/resources/phyloxml_schema/1.00//schemaDiagrams/h-2043228153.map--><map name="h-2043228153">
5665 <script type="text/javascript">
5667 setState('h1408823200_diagram', true);
5671 <div class="schemaComponent box">
5673 <input type="button" id="h1408823200_scbox_button" class="control"
5674 onclick="switchState('h1408823200_scbox'); return false;"
5675 style="display: none"/>
5676 <span class="caption">Schema Component Representation</span>
5678 <div id="h1408823200_scbox" class="contents">
5679 <div style="margin-left: 0em"><<span class="scTag">xs:simpleType</span>
5680 <span class="scTag">name</span>="<span class="scContent">SequenceType</span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:restriction</span>
5681 <span class="scTag">base</span>="<span class="scContent">
5683 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
5684 </span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5685 <span class="scTag">value</span>="<span class="scContent">rna</span>"/></div>
5686 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5687 <span class="scTag">value</span>="<span class="scContent">dna</span>"/></div>
5688 <div style="margin-left: 1.5em"><<span class="scTag">xs:enumeration</span>
5689 <span class="scTag">value</span>="<span class="scContent">aa</span>"/></div></<span class="scTag">xs:restriction</span>></div></<span class="scTag">xs:simpleType</span>></div>
5691 <script type="text/javascript">
5693 setState('h1408823200_scbox', false);
5697 <div style="text-align: right; clear: both;">
5698 <a href="#top">top</a>
5701 <h3>Simple Type: <a name="h712147427" class="name">TaxonomyCode</a>
5703 <table class="hierarchy">
5705 <th>Super-types:</th>
5708 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span> < <strong>TaxonomyCode</strong> (by restriction)</td>
5715 <table class="properties">
5718 <td>TaxonomyCode</td>
5721 <th>Used by (from the same schema document)</th>
5722 <td>Complex Type <b>
5723 <a href="#h888650454">Taxonomy</a>
5731 <li>Base XSD Type: token</li>
5735 <em>pattern</em> = [a-zA-Z0-9_]{2,10}</li>
5740 <div class="sample box">
5742 <input type="button" id="h712147427_diagram_button" class="control"
5743 onclick="switchState('h712147427_diagram'); return false;"
5744 style="display: none"/>
5745 <span class="caption">Diagram</span>
5747 <div id="h712147427_diagram" class="contents">
5748 <img usemap="#h516707748" src="schemaDiagrams/h516707748.png"/>
5750 Map ref: file:/D:/WORK/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester-atv/resources/phyloxml_schema/1.00//schemaDiagrams/h516707748.map--><map name="h516707748">
5753 <script type="text/javascript">
5755 setState('h712147427_diagram', true);
5759 <div class="schemaComponent box">
5761 <input type="button" id="h712147427_scbox_button" class="control"
5762 onclick="switchState('h712147427_scbox'); return false;"
5763 style="display: none"/>
5764 <span class="caption">Schema Component Representation</span>
5766 <div id="h712147427_scbox" class="contents">
5767 <div style="margin-left: 0em"><<span class="scTag">xs:simpleType</span>
5768 <span class="scTag">name</span>="<span class="scContent">TaxonomyCode</span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:restriction</span>
5769 <span class="scTag">base</span>="<span class="scContent">
5771 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
5772 </span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:pattern</span>
5773 <span class="scTag">value</span>="<span class="scContent">[a-zA-Z0-9_]{2,10}</span>"/></div></<span class="scTag">xs:restriction</span>></div></<span class="scTag">xs:simpleType</span>></div>
5775 <script type="text/javascript">
5777 setState('h712147427_scbox', false);
5781 <div style="text-align: right; clear: both;">
5782 <a href="#top">top</a>
5785 <h3>Simple Type: <a name="h577349652" class="name">id_ref</a>
5787 <table class="hierarchy">
5789 <th>Super-types:</th>
5792 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:IDREF</span> < <strong>id_ref</strong> (by restriction)</td>
5799 <table class="properties">
5805 <th>Used by (from the same schema document)</th>
5806 <td>Complex Type <b>
5807 <a href="#h-1794244794">Sequence</a>
5808 </b>, Complex Type <b>
5809 <a href="#h158033242">Property</a>
5810 </b>, Complex Type <b>
5811 <a href="#h-802965662">SequenceRelation</a>
5812 </b>, Complex Type <b>
5813 <a href="#h-802965662">SequenceRelation</a>
5814 </b>, Complex Type <b>
5815 <a href="#h192331856">CladeRelation</a>
5816 </b>, Complex Type <b>
5817 <a href="#h192331856">CladeRelation</a>
5825 <li>Base XSD Type: IDREF</li>
5830 <div class="sample box">
5832 <input type="button" id="h577349652_diagram_button" class="control"
5833 onclick="switchState('h577349652_diagram'); return false;"
5834 style="display: none"/>
5835 <span class="caption">Diagram</span>
5837 <div id="h577349652_diagram" class="contents">
5838 <img usemap="#h813803539" src="schemaDiagrams/h813803539.png"/>
5840 Map ref: file:/D:/WORK/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester-atv/resources/phyloxml_schema/1.00//schemaDiagrams/h813803539.map--><map name="h813803539">
5843 <script type="text/javascript">
5845 setState('h577349652_diagram', true);
5849 <div class="schemaComponent box">
5851 <input type="button" id="h577349652_scbox_button" class="control"
5852 onclick="switchState('h577349652_scbox'); return false;"
5853 style="display: none"/>
5854 <span class="caption">Schema Component Representation</span>
5856 <div id="h577349652_scbox" class="contents">
5857 <div style="margin-left: 0em"><<span class="scTag">xs:simpleType</span>
5858 <span class="scTag">name</span>="<span class="scContent">id_ref</span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:restriction</span>
5859 <span class="scTag">base</span>="<span class="scContent">
5861 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:IDREF</span>
5862 </span>"/></div></<span class="scTag">xs:simpleType</span>></div>
5864 <script type="text/javascript">
5866 setState('h577349652_scbox', false);
5870 <div style="text-align: right; clear: both;">
5871 <a href="#top">top</a>
5874 <h3>Simple Type: <a name="h-1482113798" class="name">id_source</a>
5876 <table class="hierarchy">
5878 <th>Super-types:</th>
5881 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:ID</span> < <strong>id_source</strong> (by restriction)</td>
5888 <table class="properties">
5894 <th>Used by (from the same schema document)</th>
5895 <td>Complex Type <b>
5896 <a href="#h-1124608460">Clade</a>
5897 </b>, Complex Type <b>
5898 <a href="#h888650454">Taxonomy</a>
5899 </b>, Complex Type <b>
5900 <a href="#h-1794244794">Sequence</a>
5908 <li>Base XSD Type: ID</li>
5913 <div class="sample box">
5915 <input type="button" id="h-1482113798_diagram_button" class="control"
5916 onclick="switchState('h-1482113798_diagram'); return false;"
5917 style="display: none"/>
5918 <span class="caption">Diagram</span>
5920 <div id="h-1482113798_diagram" class="contents">
5921 <img usemap="#h123518701" src="schemaDiagrams/h123518701.png"/>
5923 Map ref: file:/D:/WORK/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester-atv/resources/phyloxml_schema/1.00//schemaDiagrams/h123518701.map--><map name="h123518701">
5926 <script type="text/javascript">
5928 setState('h-1482113798_diagram', true);
5932 <div class="schemaComponent box">
5934 <input type="button" id="h-1482113798_scbox_button" class="control"
5935 onclick="switchState('h-1482113798_scbox'); return false;"
5936 style="display: none"/>
5937 <span class="caption">Schema Component Representation</span>
5939 <div id="h-1482113798_scbox" class="contents">
5940 <div style="margin-left: 0em"><<span class="scTag">xs:simpleType</span>
5941 <span class="scTag">name</span>="<span class="scContent">id_source</span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:restriction</span>
5942 <span class="scTag">base</span>="<span class="scContent">
5944 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:ID</span>
5945 </span>"/></div></<span class="scTag">xs:simpleType</span>></div>
5947 <script type="text/javascript">
5949 setState('h-1482113798_scbox', false);
5953 <div style="text-align: right; clear: both;">
5954 <a href="#top">top</a>
5957 <h3>Simple Type: <a name="h-675984882" class="name">ref</a>
5959 <table class="hierarchy">
5961 <th>Super-types:</th>
5964 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span> < <strong>ref</strong> (by restriction)</td>
5971 <table class="properties">
5977 <th>Used by (from the same schema document)</th>
5978 <td>Complex Type <b>
5979 <a href="#h917087604">Annotation</a>
5980 </b>, Complex Type <b>
5981 <a href="#h158033242">Property</a>
5982 </b>, Complex Type <b>
5983 <a href="#h158033242">Property</a>
5991 <li>Base XSD Type: token</li>
5995 <em>pattern</em> = [a-zA-Z0-9_]+:[a-zA-Z0-9_\.\-\s]+</li>
6000 <div class="sample box">
6002 <input type="button" id="h-675984882_diagram_button" class="control"
6003 onclick="switchState('h-675984882_diagram'); return false;"
6004 style="display: none"/>
6005 <span class="caption">Diagram</span>
6007 <div id="h-675984882_diagram" class="contents">
6008 <img usemap="#h-1056119207" src="schemaDiagrams/h-1056119207.png"/>
6010 Map ref: file:/D:/WORK/SOFTWARE_DEV/ECLIPSE_WORKSPACE/forester-atv/resources/phyloxml_schema/1.00//schemaDiagrams/h-1056119207.map--><map name="h-1056119207">
6013 <script type="text/javascript">
6015 setState('h-675984882_diagram', true);
6019 <div class="schemaComponent box">
6021 <input type="button" id="h-675984882_scbox_button" class="control"
6022 onclick="switchState('h-675984882_scbox'); return false;"
6023 style="display: none"/>
6024 <span class="caption">Schema Component Representation</span>
6026 <div id="h-675984882_scbox" class="contents">
6027 <div style="margin-left: 0em"><<span class="scTag">xs:simpleType</span>
6028 <span class="scTag">name</span>="<span class="scContent">ref</span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:restriction</span>
6029 <span class="scTag">base</span>="<span class="scContent">
6031 <a href="#ns_xs" title="Find out namespace of 'xs' prefix">xs</a>:token</span>
6032 </span>"><div style="margin-left: 1.5em"><<span class="scTag">xs:pattern</span>
6033 <span class="scTag">value</span>="<span class="scContent">[a-zA-Z0-9_]+:[a-zA-Z0-9_\.\-\s]+</span>"/></div></<span class="scTag">xs:restriction</span>></div></<span class="scTag">xs:simpleType</span>></div>
6035 <script type="text/javascript">
6037 setState('h-675984882_scbox', false);
6041 <div style="text-align: right; clear: both;">
6042 <a href="#top">top</a>
6047 <a name="Legend">Legend</a>
6049 <div style="float: left; width: 15em;">
6050 <h3 style="margin-bottom: 0px;">Complex Type:</h3>
6051 <div class="hint" style="margin-left: 0em;">Schema Component Type</div>
6053 <div style="float: left; width: 15em;">
6054 <h3 style="margin-bottom: 0px;">
6055 <span class="name">AusAddress</span>
6057 <div class="hint" style="margin-left: 0em;">Schema Component Name</div>
6059 <table class="hierarchy" style="clear : both">
6061 <th>Super-types:</th>
6063 <span class="type" style="color: #0000FF; text-decoration:underline;">Address</span> < <span class="current">AusAddress</span> (by extension)</td>
6070 <span class="type" style="color: #0000FF; text-decoration:underline;">QLDAddress</span> (by restriction)</li>
6075 <div class="hint">If this schema component is a type definition, its type hierarchy is shown in a gray-bordered box.</div>
6076 <table class="properties">
6083 <a title="Look up 'Abstract' in glossary" href="phyloxml.xsd.html#term_Abstract">Abstract</a>
6088 <div class="hint">The table above displays the properties of this schema component.</div>
6089 <div class="sample box">
6091 <span class="caption">XML Instance Representation</span>
6093 <div class="contents">
6094 <span style="margin-left: 0em"><...</span>
6095 <span class="newFields">
6096 <span> country="<span class="fixed">Australia</span>"</span>
6098 <span style="margin-left: 1.5em" class="inherited"><unitNo> <span class="type">string</span> </unitNo> <span class="occurs">[0..1]</span>
6101 <span style="margin-left: 1.5em" class="inherited"><houseNo> <span class="type">string</span> </houseNo> <span class="occurs">[1]</span>
6104 <span style="margin-left: 1.5em" class="inherited"><street> <span class="type">string</span> </street> <span class="occurs">[1]</span>
6107 <span class="group" style="margin-left: 1.5em">Start <a title="Look up 'Choice' in glossary" href="#term_Choice">Choice</a>
6108 <span class="occurs">[1]</span>
6111 <span style="margin-left: 3em" class="inherited"><city> <span class="type">string</span> </city> <span class="occurs">[1]</span>
6114 <span style="margin-left: 3em" class="inherited"><town> <span class="type">string</span> </town> <span class="occurs">[1]</span>
6117 <span class="group" style="margin-left: 1.5em">End Choice</span>
6119 <span class="newFields">
6120 <span style="margin-left: 1.5em"><state> <span class="type" style="text-decoration:underline;">AusStates</span> </state> <span class="occurs">[1]</span>
6123 <span style="margin-left: 1.5em"><postcode> <span class="constraint">string <<<em>pattern</em> = [1-9][0-9]{3}>></span> </postcode> <span class="occurs">[1]</span>
6124 <a href="javascript:void(0)" title="View Documentation" class="documentation"
6125 onclick="docArray = new Array('Post code must be a four-digit number.'); viewDocumentation('Element', 'postcode', docArray);">?</a>
6129 <span style="margin-left: 0em"></...></span>
6134 <p>The XML Instance Representation table above shows the schema component's content as an XML instance.</p>
6136 <li>The minimum and maximum occurrence of elements and attributes are provided in square brackets, e.g. [0..1].</li>
6137 <li>Model group information are shown in gray, e.g. Start Choice ... End Choice.</li>
6138 <li>For type derivations, the elements and attributes that have been added to or changed from the base type's content are shown in <span style="font-weight: bold">bold</span>.</li>
6139 <li>If an element/attribute has a fixed value, the fixed value is shown in green, e.g. country="Australia".</li>
6140 <li>Otherwise, the type of the element/attribute is displayed.
6142 <li>If the element/attribute's type is in the schema, a link is provided to it.</li>
6143 <li>For local simple type definitions, the constraints are displayed in angle brackets, e.g. <<<em>pattern</em> = [1-9][0-9]{3}>>.</li>
6146 <li>If a local element/attribute has documentation, it will be displayed in a window that pops up when the question mark inside the attribute or next to the element is clicked, e.g. <postcode>.</li>
6149 <div class="schemaComponent box">
6151 <span class="caption">Schema Component Representation</span>
6153 <div class="contents">
6154 <span style="margin-left: 0em"><<span class="scTag">complexType</span>
6155 <span class="scTag">name</span>="<span class="scContent">AusAddress</span>"></span>
6157 <span style="margin-left: 1.5em"><<span class="scTag">complexContent</span>></span>
6159 <span style="margin-left: 3em"><<span class="scTag">extension</span>
6160 <span class="scTag">base</span>="<span class="scContent">
6161 <span class="type" style="text-decoration:underline;">Address</span>
6164 <span style="margin-left: 4.5em"><<span class="scTag">sequence</span>></span>
6166 <span style="margin-left: 6em"><<span class="scTag">element</span>
6167 <span class="scTag">name</span>="<span class="scContent">state</span>" <span class="scTag">type</span>="<span class="scContent">
6168 <span class="type" style="text-decoration:underline;">AusStates</span>
6169 </span>"/></span>
6171 <span style="margin-left: 6em"><<span class="scTag">element</span>
6172 <span class="scTag">name</span>="<span class="scContent">postcode</span>"></span>
6174 <span style="margin-left: 7.5em"><<span class="scTag">simpleType</span>></span>
6176 <span style="margin-left: 9em"><<span class="scTag">restriction</span>
6177 <span class="scTag">base</span>="<span class="scContent">
6178 <span class="type">string</span>
6181 <span style="margin-left: 10.5em"><<span class="scTag">pattern</span>
6182 <span class="scTag">value</span>="<span class="scContent">[1-9][0-9]{3}</span>"/></span>
6184 <span style="margin-left: 9em"></<span class="scTag">restriction</span>></span>
6186 <span style="margin-left: 7.5em"></<span class="scTag">simpleType</span>></span>
6188 <span style="margin-left: 6em"></<span class="scTag">element</span>></span>
6190 <span style="margin-left: 4.5em"></<span class="scTag">sequence</span>></span>
6192 <span style="margin-left: 4.5em"><<span class="scTag">attribute</span>
6193 <span class="scTag">name</span>="<span class="scContent">country</span>" <span class="scTag">type</span>="<span class="scContent">
6194 <span class="type">string</span>
6195 </span>" <span class="scTag">fixed</span>="<span class="scContent">Australia</span>"/></span>
6197 <span style="margin-left: 3em"></<span class="scTag">extension</span>></span>
6199 <span style="margin-left: 1.5em"></<span class="scTag">complexContent</span>></span>
6201 <span style="margin-left: 0em"></<span class="scTag">complexType</span>></span>
6205 <div class="hint">The Schema Component Representation table above displays the underlying XML representation of the schema component. (Annotations are not shown.)</div>
6206 <div style="text-align: right; clear: both;">
6207 <a href="#top">top</a>
6213 <a name="Glossary">Glossary</a>
6216 <span class="glossaryTerm">
6217 <a name="term_Abstract">Abstract</a>
6218 </span>(Applies to complex type definitions and element declarations). An abstract element or complex type cannot used to validate an element instance. If there is a reference to an abstract element, only element declarations that can substitute the abstract element can be used to validate the instance. For references to abstract type definitions, only derived types can be used.</p>
6220 <span class="glossaryTerm">
6221 <a name="term_All">All Model Group</a>
6222 </span>Child elements can be provided <em>in any order</em> in instances. See: <a title="http://www.w3.org/TR/xmlschema-1/#element-all"
6223 href="http://www.w3.org/TR/xmlschema-1/#element-all">http://www.w3.org/TR/xmlschema-1/#element-all</a>.</p>
6225 <span class="glossaryTerm">
6226 <a name="term_Choice">Choice Model Group</a>
6228 <em>Only one</em> from the list of child elements and model groups can be provided in instances. See: <a title="http://www.w3.org/TR/xmlschema-1/#element-choice"
6229 href="http://www.w3.org/TR/xmlschema-1/#element-choice">http://www.w3.org/TR/xmlschema-1/#element-choice</a>.</p>
6231 <span class="glossaryTerm">
6232 <a name="term_CollapseWS">Collapse Whitespace Policy</a>
6233 </span>Replace tab, line feed, and carriage return characters with space character (Unicode character 32). Then, collapse contiguous sequences of space characters into single space character, and remove leading and trailing space characters.</p>
6235 <span class="glossaryTerm">
6236 <a name="term_ElemBlock">Disallowed Substitutions</a>
6237 </span>(Applies to element declarations). If <em>substitution</em> is specified, then <a title="Look up 'substitution group' in glossary"
6238 href="phyloxml.xsd.html#term_SubGroup">substitution group</a> members cannot be used in place of the given element declaration to validate element instances. If <em>derivation methods</em>, e.g. extension, restriction, are specified, then the given element declaration will not validate element instances that have types derived from the element declaration's type using the specified derivation methods. Normally, element instances can override their declaration's type by specifying an <code>xsi:type</code> attribute.</p>
6240 <span class="glossaryTerm">
6241 <a name="term_Key">Key Constraint</a>
6242 </span>Like <a title="Look up 'Uniqueness Constraint' in glossary"
6243 href="phyloxml.xsd.html#term_Unique">Uniqueness Constraint</a>, but additionally requires that the specified value(s) must be provided. See: <a title="http://www.w3.org/TR/xmlschema-1/#cIdentity-constraint_Definitions"
6244 href="http://www.w3.org/TR/xmlschema-1/#cIdentity-constraint_Definitions">http://www.w3.org/TR/xmlschema-1/#cIdentity-constraint_Definitions</a>.</p>
6246 <span class="glossaryTerm">
6247 <a name="term_KeyRef">Key Reference Constraint</a>
6248 </span>Ensures that the specified value(s) must match value(s) from a <a title="Look up 'Key Constraint' in glossary" href="phyloxml.xsd.html#term_Key">Key Constraint</a> or <a title="Look up 'Uniqueness Constraint' in glossary"
6249 href="phyloxml.xsd.html#term_Unique">Uniqueness Constraint</a>. See: <a title="http://www.w3.org/TR/xmlschema-1/#cIdentity-constraint_Definitions"
6250 href="http://www.w3.org/TR/xmlschema-1/#cIdentity-constraint_Definitions">http://www.w3.org/TR/xmlschema-1/#cIdentity-constraint_Definitions</a>.</p>
6252 <span class="glossaryTerm">
6253 <a name="term_ModelGroup">Model Group</a>
6254 </span>Groups together element content, specifying the order in which the element content can occur and the number of times the group of element content may be repeated. See: <a title="http://www.w3.org/TR/xmlschema-1/#Model_Groups"
6255 href="http://www.w3.org/TR/xmlschema-1/#Model_Groups">http://www.w3.org/TR/xmlschema-1/#Model_Groups</a>.</p>
6257 <span class="glossaryTerm">
6258 <a name="term_Nillable">Nillable</a>
6259 </span>(Applies to element declarations). If an element declaration is nillable, instances can use the <code>xsi:nil</code> attribute. The <code>xsi:nil</code> attribute is the boolean attribute, <em>nil</em>, from the <em>http://www.w3.org/2001/XMLSchema-instance</em> namespace. If an element instance has an <code>xsi:nil</code> attribute set to true, it can be left empty, even though its element declaration may have required content.</p>
6261 <span class="glossaryTerm">
6262 <a name="term_Notation">Notation</a>
6263 </span>A notation is used to identify the format of a piece of data. Values of elements and attributes that are of type, NOTATION, must come from the names of declared notations. See: <a title="http://www.w3.org/TR/xmlschema-1/#cNotation_Declarations"
6264 href="http://www.w3.org/TR/xmlschema-1/#cNotation_Declarations">http://www.w3.org/TR/xmlschema-1/#cNotation_Declarations</a>.</p>
6266 <span class="glossaryTerm">
6267 <a name="term_PreserveWS">Preserve Whitespace Policy</a>
6268 </span>Preserve whitespaces exactly as they appear in instances.</p>
6270 <span class="glossaryTerm">
6271 <a name="term_TypeFinal">Prohibited Derivations</a>
6272 </span>(Applies to type definitions). Derivation methods that cannot be used to create sub-types from a given type definition.</p>
6274 <span class="glossaryTerm">
6275 <a name="term_TypeBlock">Prohibited Substitutions</a>
6276 </span>(Applies to complex type definitions). Prevents sub-types that have been derived using the specified derivation methods from validating element instances in place of the given type definition.</p>
6278 <span class="glossaryTerm">
6279 <a name="term_ReplaceWS">Replace Whitespace Policy</a>
6280 </span>Replace tab, line feed, and carriage return characters with space character (Unicode character 32).</p>
6282 <span class="glossaryTerm">
6283 <a name="term_Sequence">Sequence Model Group</a>
6284 </span>Child elements and model groups must be provided <em>in the specified order</em> in instances. See: <a title="http://www.w3.org/TR/xmlschema-1/#element-sequence"
6285 href="http://www.w3.org/TR/xmlschema-1/#element-sequence">http://www.w3.org/TR/xmlschema-1/#element-sequence</a>.</p>
6287 <span class="glossaryTerm">
6288 <a name="term_SubGroup">Substitution Group</a>
6289 </span>Elements that are <em>members</em> of a substitution group can be used wherever the <em>head</em> element of the substitution group is referenced.</p>
6291 <span class="glossaryTerm">
6292 <a name="term_ElemFinal">Substitution Group Exclusions</a>
6293 </span>(Applies to element declarations). Prohibits element declarations from nominating themselves as being able to substitute a given element declaration, if they have types that are derived from the original element's type using the specified derivation methods.</p>
6295 <span class="glossaryTerm">
6296 <a name="term_TargetNS">Target Namespace</a>
6297 </span>The target namespace identifies the namespace that components in this schema belongs to. If no target namespace is provided, then the schema components do not belong to any namespace.</p>
6299 <span class="glossaryTerm">
6300 <a name="term_Unique">Uniqueness Constraint</a>
6301 </span>Ensures uniqueness of an element/attribute value, or a combination of values, within a specified scope. See: <a title="http://www.w3.org/TR/xmlschema-1/#cIdentity-constraint_Definitions"
6302 href="http://www.w3.org/TR/xmlschema-1/#cIdentity-constraint_Definitions">http://www.w3.org/TR/xmlschema-1/#cIdentity-constraint_Definitions</a>.</p>
6303 <div style="text-align: right; clear: both;">
6304 <a href="#top">top</a>
6308 <p class="footer">Generated by <a href="http://www.oxygenxml.com"><oXygen/> XML Editor</a> using a modified version of <a href="http://titanium.dstc.edu.au/xml/xs3p">xs3p</a> that adds schema diagrams and chunking support. Last modified: <script type="text/javascript">
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