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<%-- $Id$ |
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------------------------------------------------------------------ |
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BioArray Software Environment (BASE) - http:// base.thep.lu.se/ |
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|
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This file is part of BASE - BioArray Software Environment. |
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Available at http://base.thep.lu.se/ |
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|
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BASE is free software; you can redistribute it and/or |
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modify it under the terms of the GNU General Public License |
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as published by the Free Software Foundation; either version 3 |
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of the License, or (at your option) any later version. |
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|
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BASE is distributed in the hope that it will be useful, |
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but WITHOUT ANY WARRANTY; without even the implied warranty of |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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GNU General Public License for more details. |
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|
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You should have received a copy of the GNU General Public License |
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along with BASE. If not, see <http://www.gnu.org/licenses/>. |
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------------------------------------------------------------------ |
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|
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@author Nicklas |
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@version 2.0 |
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--%> |
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<%@ page pageEncoding="UTF-8" session="false" |
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import="net.sf.basedb.core.SessionControl" |
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import="net.sf.basedb.core.DbControl" |
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import="net.sf.basedb.core.Experiment" |
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import="net.sf.basedb.core.BioAssaySet" |
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import="net.sf.basedb.core.BioAssay" |
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import="net.sf.basedb.core.RawDataType" |
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import="net.sf.basedb.core.RawDataProperty" |
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import="net.sf.basedb.core.Formula" |
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import="net.sf.basedb.core.IntensityTransform" |
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import="net.sf.basedb.core.AnnotationType" |
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import="net.sf.basedb.core.ItemQuery" |
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import="net.sf.basedb.core.ItemResultList" |
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import="net.sf.basedb.core.Include" |
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import="net.sf.basedb.core.Permission" |
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import="net.sf.basedb.core.Item" |
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import="net.sf.basedb.core.data.ReporterData" |
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import="net.sf.basedb.core.query.Orders" |
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import="net.sf.basedb.core.query.Hql" |
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import="net.sf.basedb.core.query.Restrictions" |
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import="net.sf.basedb.core.query.Restriction" |
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import="net.sf.basedb.core.query.Expressions" |
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import="net.sf.basedb.clients.web.ExperimentExplorer" |
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import="net.sf.basedb.clients.web.Base" |
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import="net.sf.basedb.clients.web.DynamicUtil" |
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import="net.sf.basedb.clients.web.util.HTML" |
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import="net.sf.basedb.util.Values" |
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import="net.sf.basedb.clients.web.WebException" |
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import="net.sf.basedb.clients.web.taglib.table.TableColumn" |
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import="java.util.List" |
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import="java.util.LinkedList" |
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%> |
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<%@ taglib prefix="base" uri="/WEB-INF/base.tld" %> |
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<%@ taglib prefix="t" uri="/WEB-INF/tab.tld" %> |
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<%! |
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private static void addFormulaOption(StringBuilder options, String formula, String title, String description, Formula.AverageMethod avgMethod) |
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{ |
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options.append("<option value=\"").append(HTML.encodeTags(formula)).append("\""); |
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options.append(" title=\"").append(HTML.encodeTags(description)).append("\""); |
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options.append(" data-average-method=\"").append(avgMethod.name()).append("\""); |
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options.append(">").append(HTML.encodeTags(title)).append("\n"); |
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} |
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%> |
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<% |
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final SessionControl sc = Base.getExistingSessionControl(pageContext, true); |
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final float scale = Base.getScale(sc); |
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final String ID = sc.getId(); |
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final DbControl dc = sc.newDbControl(":Experiment explorer - Plotter"); |
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try |
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{ |
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final int bioAssaySetId = Values.getInt(request.getParameter("bioAssaySetId")); |
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final int reporterIndex = Values.getInt(request.getParameter("reporterIndex")); |
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final int positionIndex = Values.getInt(request.getParameter("positionIndex")); |
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final String plotType = Values.getString(request.getParameter("type"), "assay"); |
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final int annotationTypeId = Values.getInt(request.getParameter("annotationTypeId")); |
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final boolean needAverageMethod = positionIndex == ExperimentExplorer.SPOT_AVG; |
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|
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final BioAssaySet bas = BioAssaySet.getById(dc, bioAssaySetId); |
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final RawDataType rdt = bas.getRawDataType(); |
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final Experiment experiment = bas.getExperiment(); |
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final int maxRawMappings = bas.getMaxRawMappingsForSpot(); |
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final IntensityTransform transform = bas.getIntensityTransform(); |
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final ExperimentExplorer explorer = ExperimentExplorer.getExplorer(bas); |
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final ReporterData reporter = explorer.getReporter(dc, reporterIndex); |
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final List<AnnotationType> annotationTypes = explorer.getAnnotationTypes(dc, true); |
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|
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List<TableColumn> formulas = new LinkedList<TableColumn>(); |
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DynamicUtil.addSpotColumns(formulas, dc, rdt.getChannels(), transform); |
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DynamicUtil.addFormulaColumns(formulas, dc, rdt, Formula.Type.COLUMN_EXPRESSION, |
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transform, "", "", maxRawMappings == 1); |
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DynamicUtil.addExtraColumns(formulas, dc, bas, "ev", "#", "[Xtra] "); |
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if (maxRawMappings == 1) |
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{ |
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DynamicUtil.addRawDataColumns(formulas, dc, rdt, "", "", "[Raw] "); |
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} |
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|
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StringBuilder formulaOptions = new StringBuilder(); |
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for (TableColumn tc : formulas) |
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{ |
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if (tc.getJepExpression() != null && tc.getDatatype().isNumerical()) |
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{ |
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if (!needAverageMethod || tc.getAverageMethod() != Formula.AverageMethod.NONE) |
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{ |
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String jepExpression = tc.getJepExpression(); |
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addFormulaOption(formulaOptions, jepExpression, tc.getTitle(), tc.getDescription(), tc.getAverageMethod()); |
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} |
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} |
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} |
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|
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String title = HTML.encodeTags("Plot " + bas.getName()); |
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final boolean hasCreateFilePermission = sc.hasPermission(Permission.CREATE, Item.FILE); |
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%> |
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<base:page type="popup" title="<%=title%>"> |
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<base:head scripts="tabcontrol-2.js,~plotter.js" styles="tabcontrol.css" /> |
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<base:body> |
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<h1><%=title%> <base:help helpid="explorer.plotter" /></h1> |
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06 Sep 13 |
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<div id="page-data" class="datacontainer" |
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data-bioassayset="<%=bioAssaySetId %>" |
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data-reporter-index="<%=reporterIndex %>" |
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data-position-index="<%=positionIndex %>" |
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></div> |
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<form name="plot"> |
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<div class="content bottomborder"> |
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<div class="absolutefull rightborder" style="right: 550px;"> |
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|
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<table class="fullform input100 smaller"> |
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<tbody> |
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<tr> |
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<th>Plot title</th> |
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<td colspan="2"><input type="text" class="text" maxlength="255" name="title" |
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value="<%=HTML.encodeTags(bas.getName())%>"></td> |
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</tr> |
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<tr> |
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<th class="subprompt">Subtitle</th> |
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<td colspan="2"><input type="text" class="text" maxlength="255" name="subTitle" |
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value="<%=HTML.encodeTags(reporter.getName())%>"></td> |
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</tr> |
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<tr> |
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<th>Width</th> |
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<td colspan="2"><input type="text" class="text" |
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name="width" id="width" |
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style="width: 10em;" maxlength="10" value="900" |
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> (not used by preview)</td> |
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</tr> |
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<tr> |
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<th>Height</th> |
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<td colspan="2"><input type="text" class="text" |
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name="height" id="height" |
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style="width: 10em;" maxlength="10" value="600"></td> |
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</tr> |
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<tr> |
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<th class="subprompt"></th> |
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<td colspan="2"></td> |
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</tr> |
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</tbody> |
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|
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<tbody class="simplesection"> |
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<tr> |
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<th>Y-axis</th> |
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<td> |
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<select name="yPresets" id="yPresets" style="width: 25em;" |
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data-formula-id="yFormula" |
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data-label-id="yLabel" |
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> |
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<option value="">- select from list or enter formula below - |
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<%=formulaOptions.toString()%> |
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</select> |
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</td> |
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<td></td> |
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</tr> |
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<tr> |
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<th class="subprompt">Expression</th> |
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<td><input type="text" class="text required" maxlength="255" name="yFormula" id="yFormula"></td> |
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<td> |
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<base:icon |
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id="btnExpressionBuilderY" |
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06 Sep 13 |
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data-formula-id="yFormula" |
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06 Sep 13 |
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data-title="Y-axis expression" |
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data-formula-type="COLUMN_EXPRESSION" |
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data-raw-data-type="<%=rdt.getId() %>" |
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06 Sep 13 |
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data-channels="<%=rdt.getChannels() %>" |
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data-bioassayset="<%=bioAssaySetId %>" |
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image="expression_builder.png" |
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tooltip="Use the Expression builder" |
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/> |
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</td> |
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</tr> |
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<tr> |
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<th class="subprompt">Label</th> |
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<td><input type="text" class="text" maxlength="255" name="yLabel" id="yLabel"></td> |
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<td></td> |
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</tr> |
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<tr> |
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<th class="subprompt"><label for="yLog">Log scale</label></th> |
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<td><input type="checkbox" name="yLog" id="yLog" value="1"></td> |
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<td></td> |
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</tr> |
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<% |
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if (positionIndex == ExperimentExplorer.SPOT_AVG) |
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{ |
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%> |
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<tr> |
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<th class="subprompt">Average method</th> |
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13 Jan 12 |
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<td> |
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13 Jan 12 |
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<select name="averageMethod"> |
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13 Jan 12 |
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<% |
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for (Formula.AverageMethod method : Formula.AverageMethod.values()) |
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{ |
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if (method != Formula.AverageMethod.NONE) |
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{ |
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%> |
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<option value="<%=method.name()%>"><%=method.toString()%></option> |
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<% |
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} |
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} |
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%> |
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</select> |
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</td> |
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<td></td> |
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</tr> |
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<% |
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} |
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%> |
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<tr> |
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<th>X-axis</th> |
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<td> |
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<input type="radio" name="plotType" value="assay" |
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13 Jan 12 |
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id="plotTypeAssay" <%=plotType.equals("assay") ? "checked" : ""%> |
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><label for="plotTypeAssay" |
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13 Jan 12 |
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title="Creates a line/bar plot with bioassays along the x axis">Bioassays</label> |
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06 Sep 13 |
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<input type="radio" name="plotType" value="annotation" |
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13 Jan 12 |
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id="plotTypeAnnotation" <%=plotType.equals("annotation") ? "checked" : ""%> |
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13 Jan 12 |
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><label for="plotTypeAnnotation" |
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13 Jan 12 |
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title="Creates a box plot with annotation values along the x axis">Annotation</label> |
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13 Jan 12 |
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</td> |
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13 Jan 12 |
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<td></td> |
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13 Jan 12 |
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</tr> |
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<tr> |
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<th class="subprompt">Annotation</th> |
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13 Jan 12 |
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<td> |
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13 Jan 12 |
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<select name="annotationTypeId" class="selectionlist"> |
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<% |
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13 Jan 12 |
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247 |
for (AnnotationType at : annotationTypes) |
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16 Oct 09 |
nicklas |
248 |
{ |
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13 Jan 12 |
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249 |
String selected = at.getId() == annotationTypeId ? "selected" : ""; |
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13 Jan 12 |
nicklas |
250 |
%> |
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13 Jan 12 |
nicklas |
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<option value="<%=at.getId()%>" <%=selected%>><%=HTML.encodeTags(at.getName())%> |
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13 Jan 12 |
nicklas |
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<% |
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16 Oct 09 |
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} |
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16 Oct 09 |
nicklas |
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%> |
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16 Oct 09 |
nicklas |
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</select> |
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16 Oct 09 |
nicklas |
256 |
</td> |
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13 Jan 12 |
nicklas |
257 |
<td></td> |
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13 Jan 12 |
nicklas |
258 |
</tr> |
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13 Jan 12 |
nicklas |
259 |
<tr> |
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13 Jan 12 |
nicklas |
260 |
<th class="subprompt"><label for="hideXLabels">No labels</label></th> |
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13 Jan 12 |
nicklas |
261 |
<td><input type="checkbox" name="hideXLabels" id="hideXLabels" value="1"></td> |
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13 Jan 12 |
nicklas |
262 |
<td></td> |
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13 Jan 12 |
nicklas |
263 |
</tr> |
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13 Jan 12 |
nicklas |
264 |
<tr> |
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13 Jan 12 |
nicklas |
265 |
<th>Plot type</th> |
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13 Jan 12 |
nicklas |
266 |
<td> |
5924 |
13 Jan 12 |
nicklas |
267 |
<select name="subtype"> |
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13 Jan 12 |
nicklas |
268 |
<option value="line">Line plot</option> |
5924 |
13 Jan 12 |
nicklas |
269 |
<option value="bar">Bar plot</option> |
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13 Jan 12 |
nicklas |
270 |
</select> |
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13 Jan 12 |
nicklas |
271 |
<td></td> |
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13 Jan 12 |
nicklas |
272 |
</tr> |
5924 |
13 Jan 12 |
nicklas |
273 |
</tbody> |
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13 Jan 12 |
nicklas |
274 |
|
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13 Jan 12 |
nicklas |
275 |
<tr class="dynamic"> |
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13 Jan 12 |
nicklas |
276 |
<th></th> |
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13 Jan 12 |
nicklas |
277 |
<td colspan="2"></td> |
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16 Oct 09 |
nicklas |
278 |
</tr> |
5138 |
16 Oct 09 |
nicklas |
279 |
</table> |
5924 |
13 Jan 12 |
nicklas |
280 |
|
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02 Oct 09 |
nicklas |
281 |
</div> |
6612 |
21 Nov 14 |
nicklas |
282 |
<div class="absolutefull bg-filled-50" style="width: 550px; left: auto;"> |
5924 |
13 Jan 12 |
nicklas |
283 |
<img src="../../../../images/plot_empty.png" id="preview" |
6143 |
20 Sep 12 |
nicklas |
284 |
style="position: absolute; top: 5px; z-index: 1;" alt=""> |
5924 |
13 Jan 12 |
nicklas |
285 |
<img src="../../../../images/plot_select.png" id="overlay" |
6143 |
20 Sep 12 |
nicklas |
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style="position: absolute; top: 5px; z-index: 2;" alt=""> |
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13 Jan 12 |
nicklas |
287 |
</div> |
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02 Oct 09 |
nicklas |
288 |
|
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13 Jan 12 |
nicklas |
289 |
</div> |
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13 Jan 12 |
nicklas |
290 |
</form> |
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13 Jan 12 |
nicklas |
291 |
|
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13 Jan 12 |
nicklas |
292 |
<base:buttongroup subclass="dialogbuttons"> |
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06 Sep 13 |
nicklas |
293 |
<base:button |
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06 Sep 13 |
nicklas |
294 |
id="btnPreviewPlot" |
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06 Sep 13 |
nicklas |
295 |
title="Preview" |
6315 |
06 Sep 13 |
nicklas |
296 |
image="plotter_preview.png" |
6315 |
06 Sep 13 |
nicklas |
297 |
tooltip="Generate a preview of the plot" |
5924 |
13 Jan 12 |
nicklas |
298 |
/> |
6315 |
06 Sep 13 |
nicklas |
299 |
<base:button |
6315 |
06 Sep 13 |
nicklas |
300 |
id="btnViewPlot" |
6315 |
06 Sep 13 |
nicklas |
301 |
title="View…" |
6315 |
06 Sep 13 |
nicklas |
302 |
image="plotter.png" |
6315 |
06 Sep 13 |
nicklas |
303 |
tooltip="View a fullsized version of the plot (in a popup)" |
5924 |
13 Jan 12 |
nicklas |
304 |
/> |
6315 |
06 Sep 13 |
nicklas |
305 |
<base:button |
6315 |
06 Sep 13 |
nicklas |
306 |
id="btnDownloadPlot" |
6315 |
06 Sep 13 |
nicklas |
307 |
title="Download…" |
5946 |
03 Feb 12 |
nicklas |
308 |
image="download.png" |
5924 |
13 Jan 12 |
nicklas |
309 |
tooltip="Downlad a fullsized version of the plot to your computer" |
5924 |
13 Jan 12 |
nicklas |
310 |
/> |
6315 |
06 Sep 13 |
nicklas |
311 |
<base:button |
6315 |
06 Sep 13 |
nicklas |
312 |
id="btnSavePlot" |
6315 |
06 Sep 13 |
nicklas |
313 |
title="Save as…" |
5946 |
03 Feb 12 |
nicklas |
314 |
image="saveas.png" |
5924 |
13 Jan 12 |
nicklas |
315 |
disabled="<%=!hasCreateFilePermission%>" |
5924 |
13 Jan 12 |
nicklas |
316 |
tooltip="<%=hasCreateFilePermission ? |
5924 |
13 Jan 12 |
nicklas |
317 |
"Save a fullsized version of the plot on the BASE server" : |
5924 |
13 Jan 12 |
nicklas |
318 |
"You don't have permission to create files" %>" |
5924 |
13 Jan 12 |
nicklas |
319 |
/> |
6315 |
06 Sep 13 |
nicklas |
320 |
<base:button id="close" title="Close" /> |
5924 |
13 Jan 12 |
nicklas |
321 |
</base:buttongroup> |
5924 |
13 Jan 12 |
nicklas |
322 |
|
5114 |
02 Oct 09 |
nicklas |
323 |
</base:body> |
5114 |
02 Oct 09 |
nicklas |
324 |
</base:page> |
5114 |
02 Oct 09 |
nicklas |
325 |
<% |
5114 |
02 Oct 09 |
nicklas |
326 |
} |
5114 |
02 Oct 09 |
nicklas |
327 |
finally |
5114 |
02 Oct 09 |
nicklas |
328 |
{ |
5114 |
02 Oct 09 |
nicklas |
329 |
if (dc != null) dc.close(); |
5114 |
02 Oct 09 |
nicklas |
330 |
} |
5114 |
02 Oct 09 |
nicklas |
331 |
%> |