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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.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.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) |
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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(">").append(HTML.encodeTags(title)).append("\n"); |
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} |
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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 plotter"); |
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try |
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{ |
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int bioAssaySetId = Values.getInt(request.getParameter("bioassayset_id")); |
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int bioAssayId = Values.getInt(request.getParameter("bioassay_id")); |
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BioAssay ba = bioAssayId == 0 ? null : BioAssay.getById(dc, bioAssayId); |
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BioAssaySet bas = ba == null ? BioAssaySet.getById(dc, bioAssaySetId) : ba.getBioAssaySet(); |
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RawDataType rdt = bas.getRawDataType(); |
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Experiment experiment = bas.getExperiment(); |
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int maxRawMappings = bas.getMaxRawMappingsForSpot(); |
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IntensityTransform transform = bas.getIntensityTransform(); |
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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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String jepExpression = tc.getJepExpression(); |
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addFormulaOption(formulaOptions, jepExpression, tc.getTitle(), tc.getDescription()); |
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} |
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} |
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|
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StringBuilder filterOptions = new StringBuilder(); |
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ItemQuery<Formula> formulaQuery = Formula.getQuery(Formula.Type.COLUMN_RESTRICTION, rdt, transform); |
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formulaQuery.order(Orders.asc(Hql.property("name"))); |
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formulaQuery.include(Include.MINE, Include.SHARED, Include.IN_PROJECT, Include.OTHERS); |
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for (Formula formula : formulaQuery.list(dc)) |
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{ |
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String f = formula.getFormulas().get(0); |
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if (maxRawMappings == 1 || !f.contains("raw(")) |
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{ |
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addFormulaOption(filterOptions, f, |
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formula.getName(), formula.getDescription()); |
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} |
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} |
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|
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// Annnotations -- experimental factors and bioassay annotations |
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final ItemQuery<AnnotationType> query = AnnotationType.getQuery(null); |
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query.join(Hql.leftJoin("experiments", Item.EXPERIMENT.getAlias())); |
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10 Nov 06 |
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query.join(Hql.innerJoin("itemTypes", "itemType")); |
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Restriction ef = Restrictions.eq( |
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Hql.alias(Item.EXPERIMENT.getAlias()), |
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Hql.entity(experiment) |
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); |
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Restriction baa = Restrictions.eq( |
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Hql.alias("itemType"), |
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Expressions.integer(Item.BIOASSAY.getValue()) |
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); |
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query.restrict(Restrictions.or(ef, baa)); |
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query.include(Include.MINE, Include.SHARED, Include.IN_PROJECT, Include.OTHERS); |
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query.order(Orders.asc(Hql.property("name"))); |
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04 Oct 06 |
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List<AnnotationType> experimentalFactors = query.list(dc); |
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|
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String title = HTML.encodeTags("Plot " + (ba == null ? bas.getName() : ba.getName())); |
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|
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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="~plotter.js" /> |
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06 Sep 13 |
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<base:body> |
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06 Sep 13 |
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<h1><%=title%> <base:help helpid="plotter" /></h1> |
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|
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<div id="page-data" class="datacontainer" |
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data-bioassayset="<%=bioAssaySetId %>" |
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06 Sep 13 |
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data-bioassay="<%=bioAssayId %>" |
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></div> |
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|
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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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<table class="fullform input100 smaller"> |
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<tbody> |
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13 Jan 12 |
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<tr> |
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13 Jan 12 |
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<th>Plot title</th> |
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<td colspan="2"><input type="text" class="text" size="30" maxlength="255" name="title" |
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value="<%=HTML.encodeTags(ba == null ? bas.getName() : ba.getName())%>"></td> |
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</tr> |
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<tr> |
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13 Jan 12 |
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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=""></td> |
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</tr> |
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13 Jan 12 |
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<tr> |
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13 Jan 12 |
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<th>Width</th> |
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<td colspan="2"><input type="text" class="text" name="width" id="width" |
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06 Sep 13 |
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style="width: 10em;" maxlength="10" value="900"> (not used by preview)</td> |
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</tr> |
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13 Jan 12 |
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<tr> |
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13 Jan 12 |
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<th>Height</th> |
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<td colspan="2"><input type="text" class="text" name="height" id="height" |
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06 Sep 13 |
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style="width: 10em;" maxlength="10" value="600"></td> |
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</tr> |
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13 Jan 12 |
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<tr> |
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13 Jan 12 |
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<th class="subprompt"></th> |
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13 Jan 12 |
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<td colspan="2"></td> |
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13 Jan 12 |
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</tr> |
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13 Jan 12 |
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</tbody> |
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13 Jan 12 |
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<tbody class="sectionheader"> |
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13 Jan 12 |
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<tr> |
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13 Jan 12 |
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<th>Plot type</th> |
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<th colspan="2"> |
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06 Sep 13 |
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<input type="radio" name="plotType" value="scatter" |
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13 Jan 12 |
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id="plotTypeScatter" checked><label for="plotTypeScatter">Scatter</label> |
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06 Sep 13 |
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<input type="radio" name="plotType" value="histogram" |
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13 Jan 12 |
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id="plotTypeHistogram"><label for="plotTypeHistogram">Histogram</label> |
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</th> |
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13 Jan 12 |
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</tr> |
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13 Jan 12 |
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</tbody> |
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13 Jan 12 |
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<tbody id="scatterSection"> |
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13 Jan 12 |
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<tr> |
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13 Jan 12 |
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<th>Y-axis</th> |
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13 Jan 12 |
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<td> |
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06 Sep 13 |
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<select name="yPresetsScatter" id="yPresetsScatter" |
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06 Sep 13 |
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class="auto-init" |
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06 Sep 13 |
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data-auto-init="formula-presets" |
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06 Sep 13 |
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data-formula-id="yFormulaScatter" |
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06 Sep 13 |
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data-label-id="yLabelScatter" |
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06 Sep 13 |
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style="width: 25em;" |
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13 Jan 12 |
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> |
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13 Jan 12 |
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<option value="">- select from list or enter formula below - |
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13 Jan 12 |
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<%=formulaOptions.toString()%> |
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13 Jan 12 |
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</select> |
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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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13 Jan 12 |
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<tr> |
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13 Jan 12 |
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<th class="subprompt">Expression</th> |
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06 Sep 13 |
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<td><input type="text" class="text required" maxlength="255" name="yFormulaScatter" id="yFormulaScatter"></td> |
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13 Jan 12 |
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<td> |
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13 Jan 12 |
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<base:icon |
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06 Sep 13 |
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id="btnExpressionBuilderYScatter" |
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06 Sep 13 |
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subclass="auto-init" |
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06 Sep 13 |
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data-auto-init="expression-builder" |
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06 Sep 13 |
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data-formula-id="yFormulaScatter" |
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06 Sep 13 |
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data-title="Y-axis expression" |
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06 Sep 13 |
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data-formula-type="COLUMN_EXPRESSION" |
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06 Sep 13 |
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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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06 Sep 13 |
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data-bioassayset="<%=bioAssaySetId %>" |
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03 Feb 12 |
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image="expression_builder.png" |
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13 Jan 12 |
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tooltip="Use the Expression builder" |
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13 Jan 12 |
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/> |
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13 Jan 12 |
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</td> |
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13 Jan 12 |
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</tr> |
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13 Jan 12 |
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224 |
<tr> |
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13 Jan 12 |
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<th class="subprompt">Y label</th> |
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06 Sep 13 |
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<td><input type="text" class="text" maxlength="255" name="yLabelScatter" id="yLabelScatter" value=""></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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13 Jan 12 |
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229 |
<tr> |
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13 Jan 12 |
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<th class="subprompt"><label for="yLogScatter">Log scale</label></th> |
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13 Jan 12 |
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<td><input type="checkbox" name="yLogScatter" id="yLogScatter" value="1"></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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13 Jan 12 |
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234 |
<tr> |
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13 Jan 12 |
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<th>X-axis</th> |
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13 Jan 12 |
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<td> |
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06 Sep 13 |
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<select name="xPresetsScatter" id="xPresetsScatter" |
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06 Sep 13 |
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238 |
class="auto-init" |
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06 Sep 13 |
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data-auto-init="formula-presets" |
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06 Sep 13 |
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data-formula-id="xFormulaScatter" |
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06 Sep 13 |
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241 |
data-label-id="xLabelScatter" |
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06 Sep 13 |
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242 |
style="width: 25em;" |
5924 |
13 Jan 12 |
nicklas |
243 |
> |
5924 |
13 Jan 12 |
nicklas |
244 |
<option value="">- select from list or enter formula below - |
5924 |
13 Jan 12 |
nicklas |
245 |
<%=formulaOptions.toString()%> |
5924 |
13 Jan 12 |
nicklas |
246 |
</select> |
5924 |
13 Jan 12 |
nicklas |
247 |
</td> |
5924 |
13 Jan 12 |
nicklas |
248 |
<td></td> |
5924 |
13 Jan 12 |
nicklas |
249 |
</tr> |
5924 |
13 Jan 12 |
nicklas |
250 |
<tr> |
5924 |
13 Jan 12 |
nicklas |
251 |
<th class="subprompt">Expression</th> |
6315 |
06 Sep 13 |
nicklas |
252 |
<td><input type="text" class="text required" maxlength="255" name="xFormulaScatter" id="xFormulaScatter"></td> |
5924 |
13 Jan 12 |
nicklas |
253 |
<td> |
5924 |
13 Jan 12 |
nicklas |
254 |
<base:icon |
6315 |
06 Sep 13 |
nicklas |
255 |
id="btnExpressionBuilderXScatter" |
6315 |
06 Sep 13 |
nicklas |
256 |
subclass="auto-init" |
6315 |
06 Sep 13 |
nicklas |
257 |
data-auto-init="expression-builder" |
6315 |
06 Sep 13 |
nicklas |
258 |
data-formula-id="xFormulaScatter" |
6315 |
06 Sep 13 |
nicklas |
259 |
data-title="X-axis expression" |
6315 |
06 Sep 13 |
nicklas |
260 |
data-formula-type="COLUMN_EXPRESSION" |
6315 |
06 Sep 13 |
nicklas |
261 |
data-raw-data-type="<%=rdt.getId() %>" |
6315 |
06 Sep 13 |
nicklas |
262 |
data-channels="<%=rdt.getChannels() %>" |
6315 |
06 Sep 13 |
nicklas |
263 |
data-bioassayset="<%=bioAssaySetId %>" |
5946 |
03 Feb 12 |
nicklas |
264 |
image="expression_builder.png" |
5924 |
13 Jan 12 |
nicklas |
265 |
tooltip="Use the Expression builder" |
5924 |
13 Jan 12 |
nicklas |
266 |
/> |
5924 |
13 Jan 12 |
nicklas |
267 |
</td> |
5924 |
13 Jan 12 |
nicklas |
268 |
</tr> |
5924 |
13 Jan 12 |
nicklas |
269 |
<tr> |
5924 |
13 Jan 12 |
nicklas |
270 |
<th class="subprompt">X label</th> |
6315 |
06 Sep 13 |
nicklas |
271 |
<td><input type="text" class="text" maxlength="255" name="xLabelScatter" id="xLabelScatter" value=""></td> |
5924 |
13 Jan 12 |
nicklas |
272 |
<td></td> |
5924 |
13 Jan 12 |
nicklas |
273 |
</tr> |
5924 |
13 Jan 12 |
nicklas |
274 |
<tr> |
5924 |
13 Jan 12 |
nicklas |
275 |
<th class="subprompt"><label for="xLogScatter">Log scale</label></th> |
5924 |
13 Jan 12 |
nicklas |
276 |
<td><input type="checkbox" name="xLogScatter" id="xLogScatter" value="1"></td> |
5924 |
13 Jan 12 |
nicklas |
277 |
<td></td> |
5924 |
13 Jan 12 |
nicklas |
278 |
</tr> |
5924 |
13 Jan 12 |
nicklas |
279 |
</tbody> |
3015 |
11 Dec 06 |
nicklas |
280 |
|
5924 |
13 Jan 12 |
nicklas |
281 |
<tbody id="histogramSection" style="display: none;"> |
5924 |
13 Jan 12 |
nicklas |
282 |
<tr> |
5924 |
13 Jan 12 |
nicklas |
283 |
<th>Y-axis</th> |
5924 |
13 Jan 12 |
nicklas |
284 |
<td> |
5924 |
13 Jan 12 |
nicklas |
285 |
<input type="radio" name="yAggregate" id="yAggregateCount" value="count" checked |
6315 |
06 Sep 13 |
nicklas |
286 |
><label for="yAggregateCount">Count</label> |
5924 |
13 Jan 12 |
nicklas |
287 |
<input type="radio" name="yAggregate" id="yAggregateMean" value="mean" |
6315 |
06 Sep 13 |
nicklas |
288 |
><label for="yAggregateMean">Mean</label> |
5924 |
13 Jan 12 |
nicklas |
289 |
</td> |
5924 |
13 Jan 12 |
nicklas |
290 |
<td></td> |
5924 |
13 Jan 12 |
nicklas |
291 |
</tr> |
5924 |
13 Jan 12 |
nicklas |
292 |
<tr> |
5924 |
13 Jan 12 |
nicklas |
293 |
<th class="subprompt">Hi-lo</th> |
5924 |
13 Jan 12 |
nicklas |
294 |
<td> |
5924 |
13 Jan 12 |
nicklas |
295 |
<input type="radio" name="hiloAggregate" id="hiloAggregateNone" value="" checked |
5924 |
13 Jan 12 |
nicklas |
296 |
><label for="hiloAggregateNone">None</label> |
5924 |
13 Jan 12 |
nicklas |
297 |
<input type="radio" name="hiloAggregate" id="hiloAggregateMinMax" value="hilomaxmin" |
5924 |
13 Jan 12 |
nicklas |
298 |
><label for="hiloAggregateMinMax">Min/Max</label> |
5924 |
13 Jan 12 |
nicklas |
299 |
<input type="radio" name="hiloAggregate" id="hiloAggregateStdev" value="hilostdev" |
5924 |
13 Jan 12 |
nicklas |
300 |
><label for="hiloAggregateStdev">Stdev</label> |
5924 |
13 Jan 12 |
nicklas |
301 |
</td> |
5924 |
13 Jan 12 |
nicklas |
302 |
<td></td> |
5924 |
13 Jan 12 |
nicklas |
303 |
</tr> |
5924 |
13 Jan 12 |
nicklas |
304 |
<tr> |
5924 |
13 Jan 12 |
nicklas |
305 |
<th class="subprompt">Presets</th> |
5924 |
13 Jan 12 |
nicklas |
306 |
<td> |
6315 |
06 Sep 13 |
nicklas |
307 |
<select name="yPresetsHistogram" id="yPresetsHistogram" |
6315 |
06 Sep 13 |
nicklas |
308 |
class="auto-init" |
6315 |
06 Sep 13 |
nicklas |
309 |
data-auto-init="formula-presets" |
6315 |
06 Sep 13 |
nicklas |
310 |
data-formula-id="yFormulaHistogram" |
6315 |
06 Sep 13 |
nicklas |
311 |
data-label-id="yLabelHistogram" |
6315 |
06 Sep 13 |
nicklas |
312 |
style="width: 25em;" |
5924 |
13 Jan 12 |
nicklas |
313 |
disabled |
5924 |
13 Jan 12 |
nicklas |
314 |
> |
5924 |
13 Jan 12 |
nicklas |
315 |
<option value="">- select from list or enter formula below - |
5924 |
13 Jan 12 |
nicklas |
316 |
<%=formulaOptions.toString()%> |
5924 |
13 Jan 12 |
nicklas |
317 |
</select> |
5924 |
13 Jan 12 |
nicklas |
318 |
</td> |
5924 |
13 Jan 12 |
nicklas |
319 |
<td></td> |
5924 |
13 Jan 12 |
nicklas |
320 |
</tr> |
5924 |
13 Jan 12 |
nicklas |
321 |
<tr> |
5924 |
13 Jan 12 |
nicklas |
322 |
<th class="subprompt">Expression</th> |
6315 |
06 Sep 13 |
nicklas |
323 |
<td><input type="text" class="text" maxlength="255" name="yFormulaHistogram" id="yFormulaHistogram" disabled></td> |
5924 |
13 Jan 12 |
nicklas |
324 |
<td> |
5924 |
13 Jan 12 |
nicklas |
325 |
<base:icon |
6315 |
06 Sep 13 |
nicklas |
326 |
id="btnExpressionBuilderYHistogram" |
6315 |
06 Sep 13 |
nicklas |
327 |
subclass="auto-init" |
6315 |
06 Sep 13 |
nicklas |
328 |
data-auto-init="expression-builder" |
6315 |
06 Sep 13 |
nicklas |
329 |
data-formula-id="yFormulaHistogram" |
6315 |
06 Sep 13 |
nicklas |
330 |
data-title="Y-axis expression" |
6315 |
06 Sep 13 |
nicklas |
331 |
data-formula-type="COLUMN_EXPRESSION" |
6315 |
06 Sep 13 |
nicklas |
332 |
data-raw-data-type="<%=rdt.getId() %>" |
6315 |
06 Sep 13 |
nicklas |
333 |
data-channels="<%=rdt.getChannels() %>" |
6315 |
06 Sep 13 |
nicklas |
334 |
data-bioassayset="<%=bioAssaySetId %>" |
5946 |
03 Feb 12 |
nicklas |
335 |
image="expression_builder.png" |
5924 |
13 Jan 12 |
nicklas |
336 |
tooltip="Use the Expression builder" |
5924 |
13 Jan 12 |
nicklas |
337 |
/> |
5924 |
13 Jan 12 |
nicklas |
338 |
</td> |
5924 |
13 Jan 12 |
nicklas |
339 |
</tr> |
5924 |
13 Jan 12 |
nicklas |
340 |
<tr> |
5924 |
13 Jan 12 |
nicklas |
341 |
<th class="subprompt">Y label</th> |
6315 |
06 Sep 13 |
nicklas |
342 |
<td><input type="text" class="text" maxlength="255" name="yLabelHistogram" id="yLabelHistogram" value="Count"></td> |
5924 |
13 Jan 12 |
nicklas |
343 |
<td></td> |
5924 |
13 Jan 12 |
nicklas |
344 |
</tr> |
5924 |
13 Jan 12 |
nicklas |
345 |
<tr> |
5924 |
13 Jan 12 |
nicklas |
346 |
<th class="subprompt"><label for="yLogHistogram">Log scale</label></th> |
5924 |
13 Jan 12 |
nicklas |
347 |
<td><input type="checkbox" name="yLogHistogram" id="yLogHistogram" value="1"></td> |
5924 |
13 Jan 12 |
nicklas |
348 |
<td></td> |
5924 |
13 Jan 12 |
nicklas |
349 |
</tr> |
5924 |
13 Jan 12 |
nicklas |
350 |
<tr> |
5924 |
13 Jan 12 |
nicklas |
351 |
<th>X-axis</th> |
5924 |
13 Jan 12 |
nicklas |
352 |
<td> |
6315 |
06 Sep 13 |
nicklas |
353 |
<select name="xPresetsHistogram" id="xPresetsHistogram" |
6315 |
06 Sep 13 |
nicklas |
354 |
class="auto-init" |
6315 |
06 Sep 13 |
nicklas |
355 |
data-auto-init="formula-presets" |
6315 |
06 Sep 13 |
nicklas |
356 |
data-formula-id="xFormulaHistogram" |
6315 |
06 Sep 13 |
nicklas |
357 |
data-label-id="xLabelHistogram" |
6315 |
06 Sep 13 |
nicklas |
358 |
style="width: 25em;" |
5924 |
13 Jan 12 |
nicklas |
359 |
> |
5924 |
13 Jan 12 |
nicklas |
360 |
<option value="">- select from list or enter formula below - |
5924 |
13 Jan 12 |
nicklas |
361 |
<%=formulaOptions.toString()%> |
5924 |
13 Jan 12 |
nicklas |
362 |
</select> |
5924 |
13 Jan 12 |
nicklas |
363 |
</td> |
5924 |
13 Jan 12 |
nicklas |
364 |
<td></td> |
5924 |
13 Jan 12 |
nicklas |
365 |
</tr> |
5924 |
13 Jan 12 |
nicklas |
366 |
<tr> |
5924 |
13 Jan 12 |
nicklas |
367 |
<th class="subprompt">Expression</th> |
6315 |
06 Sep 13 |
nicklas |
368 |
<td><input type="text" class="text required" maxlength="255" name="xFormulaHistogram" id="xFormulaHistogram"></td> |
5924 |
13 Jan 12 |
nicklas |
369 |
<td> |
5924 |
13 Jan 12 |
nicklas |
370 |
<base:icon |
6315 |
06 Sep 13 |
nicklas |
371 |
id="btnExpressionBuilderXHistogram" |
6315 |
06 Sep 13 |
nicklas |
372 |
subclass="auto-init" |
6315 |
06 Sep 13 |
nicklas |
373 |
data-auto-init="expression-builder" |
6315 |
06 Sep 13 |
nicklas |
374 |
data-formula-id="xFormulaHistogram" |
6315 |
06 Sep 13 |
nicklas |
375 |
data-title="X-axis expression" |
6315 |
06 Sep 13 |
nicklas |
376 |
data-formula-type="COLUMN_EXPRESSION" |
6315 |
06 Sep 13 |
nicklas |
377 |
data-raw-data-type="<%=rdt.getId() %>" |
6315 |
06 Sep 13 |
nicklas |
378 |
data-channels="<%=rdt.getChannels() %>" |
6315 |
06 Sep 13 |
nicklas |
379 |
data-bioassayset="<%=bioAssaySetId %>" |
5946 |
03 Feb 12 |
nicklas |
380 |
image="expression_builder.png" |
5924 |
13 Jan 12 |
nicklas |
381 |
tooltip="Use the Expression builder" |
5924 |
13 Jan 12 |
nicklas |
382 |
/> |
5924 |
13 Jan 12 |
nicklas |
383 |
</td> |
5924 |
13 Jan 12 |
nicklas |
384 |
</tr> |
5924 |
13 Jan 12 |
nicklas |
385 |
<tr> |
5924 |
13 Jan 12 |
nicklas |
386 |
<th class="subprompt">X label</th> |
6315 |
06 Sep 13 |
nicklas |
387 |
<td><input type="text" class="text" maxlength="255" name="xLabelHistogram" id="xLabelHistogram" value=""></td> |
5924 |
13 Jan 12 |
nicklas |
388 |
<td></td> |
5924 |
13 Jan 12 |
nicklas |
389 |
</tr> |
5924 |
13 Jan 12 |
nicklas |
390 |
<tr> |
5924 |
13 Jan 12 |
nicklas |
391 |
<th class="subprompt"><label for="xLogHistogram">Log scale</label></th> |
5924 |
13 Jan 12 |
nicklas |
392 |
<td><input type="checkbox" name="xLogHistogram" id="xLogHistogram" value="1"></td> |
5924 |
13 Jan 12 |
nicklas |
393 |
<td></td> |
5924 |
13 Jan 12 |
nicklas |
394 |
</tr> |
5924 |
13 Jan 12 |
nicklas |
395 |
<tr> |
5924 |
13 Jan 12 |
nicklas |
396 |
<th class="subprompt">Bin size</th> |
5924 |
13 Jan 12 |
nicklas |
397 |
<td><input type="text" class="text" name="binSize" value="1" style="width: 10em;"></td> |
5924 |
13 Jan 12 |
nicklas |
398 |
<td></td> |
5924 |
13 Jan 12 |
nicklas |
399 |
</tr> |
5924 |
13 Jan 12 |
nicklas |
400 |
</tbody> |
5924 |
13 Jan 12 |
nicklas |
401 |
<tbody> |
5924 |
13 Jan 12 |
nicklas |
402 |
<tr> |
5924 |
13 Jan 12 |
nicklas |
403 |
<th class="subprompt"></th> |
5924 |
13 Jan 12 |
nicklas |
404 |
<td colspan="2"></td> |
5924 |
13 Jan 12 |
nicklas |
405 |
</tr> |
5924 |
13 Jan 12 |
nicklas |
406 |
</tbody> |
5924 |
13 Jan 12 |
nicklas |
407 |
<tbody class="sectionheader"> |
5924 |
13 Jan 12 |
nicklas |
408 |
<tr> |
5924 |
13 Jan 12 |
nicklas |
409 |
<th colspan="3">Filter & annotations</th> |
5924 |
13 Jan 12 |
nicklas |
410 |
</tr> |
5924 |
13 Jan 12 |
nicklas |
411 |
</tbody> |
5924 |
13 Jan 12 |
nicklas |
412 |
<tbody> |
5924 |
13 Jan 12 |
nicklas |
413 |
<tr> |
5924 |
13 Jan 12 |
nicklas |
414 |
<th>Filter</th> |
5924 |
13 Jan 12 |
nicklas |
415 |
<td colspan="2"> |
6315 |
06 Sep 13 |
nicklas |
416 |
<select name="filterPresets" id="filterPresets" |
6315 |
06 Sep 13 |
nicklas |
417 |
class="auto-init" |
6315 |
06 Sep 13 |
nicklas |
418 |
data-auto-init="formula-presets" |
6315 |
06 Sep 13 |
nicklas |
419 |
data-formula-id="filter" |
6315 |
06 Sep 13 |
nicklas |
420 |
style="width: 25em;" |
5924 |
13 Jan 12 |
nicklas |
421 |
> |
5924 |
13 Jan 12 |
nicklas |
422 |
<option value="">- select from list or enter formula below - |
5924 |
13 Jan 12 |
nicklas |
423 |
<%=filterOptions.toString()%> |
5924 |
13 Jan 12 |
nicklas |
424 |
</select> |
5924 |
13 Jan 12 |
nicklas |
425 |
</td> |
5924 |
13 Jan 12 |
nicklas |
426 |
</tr> |
5924 |
13 Jan 12 |
nicklas |
427 |
<tr> |
5924 |
13 Jan 12 |
nicklas |
428 |
<th class="subprompt"></th> |
6315 |
06 Sep 13 |
nicklas |
429 |
<td><input type="text" class="text" maxlength="255" name="filter" id="filter" placeholder="leave empty to plot all values"></td> |
5924 |
13 Jan 12 |
nicklas |
430 |
<td> |
5924 |
13 Jan 12 |
nicklas |
431 |
<base:icon |
6315 |
06 Sep 13 |
nicklas |
432 |
id="btnExpressionBuilderFilter" |
6315 |
06 Sep 13 |
nicklas |
433 |
subclass="auto-init" |
6315 |
06 Sep 13 |
nicklas |
434 |
data-auto-init="expression-builder" |
6315 |
06 Sep 13 |
nicklas |
435 |
data-formula-id="filter" |
6315 |
06 Sep 13 |
nicklas |
436 |
data-title="Filter expression" |
6315 |
06 Sep 13 |
nicklas |
437 |
data-formula-type="COLUMN_RESTRICTION" |
6315 |
06 Sep 13 |
nicklas |
438 |
data-raw-data-type="<%=rdt.getId() %>" |
6315 |
06 Sep 13 |
nicklas |
439 |
data-channels="<%=rdt.getChannels() %>" |
6315 |
06 Sep 13 |
nicklas |
440 |
data-bioassayset="<%=bioAssaySetId %>" |
5946 |
03 Feb 12 |
nicklas |
441 |
image="expression_builder.png" |
5924 |
13 Jan 12 |
nicklas |
442 |
tooltip="Use the Expression builder" |
5924 |
13 Jan 12 |
nicklas |
443 |
/> |
5924 |
13 Jan 12 |
nicklas |
444 |
</td> |
5924 |
13 Jan 12 |
nicklas |
445 |
</tr> |
5924 |
13 Jan 12 |
nicklas |
446 |
<tr> |
5924 |
13 Jan 12 |
nicklas |
447 |
<th>Annotation</th> |
5924 |
13 Jan 12 |
nicklas |
448 |
<td colspan="2"> |
6315 |
06 Sep 13 |
nicklas |
449 |
<select name="annotationPresets" id="annotationPresets" style="width: 25em;"> |
5924 |
13 Jan 12 |
nicklas |
450 |
<option value="$">- none - |
5924 |
13 Jan 12 |
nicklas |
451 |
<% |
5924 |
13 Jan 12 |
nicklas |
452 |
if (ba == null) |
5924 |
13 Jan 12 |
nicklas |
453 |
{ |
5924 |
13 Jan 12 |
nicklas |
454 |
%> |
5924 |
13 Jan 12 |
nicklas |
455 |
<option value="$bioassay">Bioassay |
5924 |
13 Jan 12 |
nicklas |
456 |
<option value="$spots">Spots |
5924 |
13 Jan 12 |
nicklas |
457 |
<option value="$arrayDesign.name">Array design |
5924 |
13 Jan 12 |
nicklas |
458 |
<option value="$software.name">Software |
5924 |
13 Jan 12 |
nicklas |
459 |
<option value="$protocol.name">Protocol |
5924 |
13 Jan 12 |
nicklas |
460 |
<option value="$scan.scanner.name">Scanner |
5924 |
13 Jan 12 |
nicklas |
461 |
<option value="$scan.protocol.name">Scanning protocol |
5924 |
13 Jan 12 |
nicklas |
462 |
<option value="$scan.hybridization.protocol.name">Hybridization protocol |
5924 |
13 Jan 12 |
nicklas |
463 |
<option value="$scan.hybridization.creationEvent.eventDate">Hybridization date |
5924 |
13 Jan 12 |
nicklas |
464 |
<option value="" disabled>- annotations - |
5924 |
13 Jan 12 |
nicklas |
465 |
<% |
5924 |
13 Jan 12 |
nicklas |
466 |
for (AnnotationType at : experimentalFactors) |
5924 |
13 Jan 12 |
nicklas |
467 |
{ |
5924 |
13 Jan 12 |
nicklas |
468 |
%> |
5924 |
13 Jan 12 |
nicklas |
469 |
<option value="$<%=at.getId()%>">[A] <%=HTML.encodeTags(at.getName())%> |
5924 |
13 Jan 12 |
nicklas |
470 |
<% |
5924 |
13 Jan 12 |
nicklas |
471 |
} |
5924 |
13 Jan 12 |
nicklas |
472 |
} |
3015 |
11 Dec 06 |
nicklas |
473 |
%> |
5924 |
13 Jan 12 |
nicklas |
474 |
<option value="" disabled>- expressions - |
5924 |
13 Jan 12 |
nicklas |
475 |
<%=filterOptions.toString()%> |
5924 |
13 Jan 12 |
nicklas |
476 |
<option value="">Other... |
5924 |
13 Jan 12 |
nicklas |
477 |
</select> |
5924 |
13 Jan 12 |
nicklas |
478 |
</td> |
5924 |
13 Jan 12 |
nicklas |
479 |
</tr> |
5924 |
13 Jan 12 |
nicklas |
480 |
<tr> |
5924 |
13 Jan 12 |
nicklas |
481 |
<th class="subprompt"></th> |
6315 |
06 Sep 13 |
nicklas |
482 |
<td><input type="text" class="text" maxlength="255" name="annotationExp" id="annotationExp" disabled></td> |
5924 |
13 Jan 12 |
nicklas |
483 |
<td> |
5924 |
13 Jan 12 |
nicklas |
484 |
<base:icon |
6315 |
06 Sep 13 |
nicklas |
485 |
id="btnExpressionBuilderAnnotation" |
6315 |
06 Sep 13 |
nicklas |
486 |
subclass="auto-init" |
6315 |
06 Sep 13 |
nicklas |
487 |
data-auto-init="expression-builder" |
6315 |
06 Sep 13 |
nicklas |
488 |
data-formula-id="annotationExp" |
6315 |
06 Sep 13 |
nicklas |
489 |
data-title="Annotation filter" |
6315 |
06 Sep 13 |
nicklas |
490 |
data-formula-type="COLUMN_RESTRICTION" |
6315 |
06 Sep 13 |
nicklas |
491 |
data-raw-data-type="<%=rdt.getId() %>" |
6315 |
06 Sep 13 |
nicklas |
492 |
data-channels="<%=rdt.getChannels() %>" |
6315 |
06 Sep 13 |
nicklas |
493 |
data-bioassayset="<%=bioAssaySetId %>" |
5946 |
03 Feb 12 |
nicklas |
494 |
image="expression_builder.png" |
5924 |
13 Jan 12 |
nicklas |
495 |
tooltip="Use the Expression builder" |
5924 |
13 Jan 12 |
nicklas |
496 |
/> |
5924 |
13 Jan 12 |
nicklas |
497 |
</td> |
5924 |
13 Jan 12 |
nicklas |
498 |
</tr> |
5924 |
13 Jan 12 |
nicklas |
499 |
</tbody> |
5924 |
13 Jan 12 |
nicklas |
500 |
<tr class="dynamic"> |
5924 |
13 Jan 12 |
nicklas |
501 |
<th></th> |
5924 |
13 Jan 12 |
nicklas |
502 |
<td colspan="2"></td> |
3015 |
11 Dec 06 |
nicklas |
503 |
</tr> |
3015 |
11 Dec 06 |
nicklas |
504 |
</table> |
5924 |
13 Jan 12 |
nicklas |
505 |
</div> |
3015 |
11 Dec 06 |
nicklas |
506 |
|
6612 |
21 Nov 14 |
nicklas |
507 |
<div class="absolutefull bg-filled-50" style="width: 550px; left: auto;"> |
5924 |
13 Jan 12 |
nicklas |
508 |
|
5924 |
13 Jan 12 |
nicklas |
509 |
<img src="../../../images/plot_empty.png" id="preview" |
6143 |
20 Sep 12 |
nicklas |
510 |
style="position: absolute; top: 5px; z-index: 1;" alt=""> |
5924 |
13 Jan 12 |
nicklas |
511 |
<img src="../../../images/plot_select.png" id="overlay" |
6143 |
20 Sep 12 |
nicklas |
512 |
style="position: absolute; top: 5px; z-index: 2;" alt=""> |
5924 |
13 Jan 12 |
nicklas |
513 |
</div> |
2097 |
21 Mar 06 |
nicklas |
514 |
</div> |
5924 |
13 Jan 12 |
nicklas |
515 |
</form> |
2097 |
21 Mar 06 |
nicklas |
516 |
|
5924 |
13 Jan 12 |
nicklas |
517 |
<base:buttongroup subclass="dialogbuttons"> |
6315 |
06 Sep 13 |
nicklas |
518 |
<base:button |
6315 |
06 Sep 13 |
nicklas |
519 |
id="btnPreviewPlot" |
6315 |
06 Sep 13 |
nicklas |
520 |
title="Preview" |
6315 |
06 Sep 13 |
nicklas |
521 |
image="plotter_preview.png" |
6315 |
06 Sep 13 |
nicklas |
522 |
tooltip="Generate a preview of the plot" |
5924 |
13 Jan 12 |
nicklas |
523 |
/> |
6315 |
06 Sep 13 |
nicklas |
524 |
<base:button |
6315 |
06 Sep 13 |
nicklas |
525 |
id="btnViewPlot" |
6315 |
06 Sep 13 |
nicklas |
526 |
title="View…" |
6315 |
06 Sep 13 |
nicklas |
527 |
image="plotter.png" |
6315 |
06 Sep 13 |
nicklas |
528 |
tooltip="View a fullsized version of the plot (in a popup)" |
5924 |
13 Jan 12 |
nicklas |
529 |
/> |
6315 |
06 Sep 13 |
nicklas |
530 |
<base:button |
6315 |
06 Sep 13 |
nicklas |
531 |
id="btnDownloadPlot" |
6315 |
06 Sep 13 |
nicklas |
532 |
title="Download…" |
5946 |
03 Feb 12 |
nicklas |
533 |
image="download.png" |
5924 |
13 Jan 12 |
nicklas |
534 |
tooltip="Downlad a fullsized version of the plot to your computer" |
5924 |
13 Jan 12 |
nicklas |
535 |
/> |
6315 |
06 Sep 13 |
nicklas |
536 |
<base:button |
6315 |
06 Sep 13 |
nicklas |
537 |
id="btnSavePlot" |
6315 |
06 Sep 13 |
nicklas |
538 |
title="Save as…" |
5946 |
03 Feb 12 |
nicklas |
539 |
image="saveas.png" |
5924 |
13 Jan 12 |
nicklas |
540 |
disabled="<%=!hasCreateFilePermission%>" |
5924 |
13 Jan 12 |
nicklas |
541 |
tooltip="<%=hasCreateFilePermission ? |
5924 |
13 Jan 12 |
nicklas |
542 |
"Save a fullsized version of the plot on the BASE server" : |
5924 |
13 Jan 12 |
nicklas |
543 |
"You don't have permission to create files" %>" |
5924 |
13 Jan 12 |
nicklas |
544 |
/> |
6315 |
06 Sep 13 |
nicklas |
545 |
<base:button id="close" title="Close" /> |
5924 |
13 Jan 12 |
nicklas |
546 |
</base:buttongroup> |
5924 |
13 Jan 12 |
nicklas |
547 |
|
2097 |
21 Mar 06 |
nicklas |
548 |
</base:body> |
2097 |
21 Mar 06 |
nicklas |
549 |
</base:page> |
2097 |
21 Mar 06 |
nicklas |
550 |
<% |
2097 |
21 Mar 06 |
nicklas |
551 |
} |
2097 |
21 Mar 06 |
nicklas |
552 |
finally |
2097 |
21 Mar 06 |
nicklas |
553 |
{ |
2097 |
21 Mar 06 |
nicklas |
554 |
if (dc != null) dc.close(); |
2097 |
21 Mar 06 |
nicklas |
555 |
} |
2097 |
21 Mar 06 |
nicklas |
556 |
%> |