edu.scripps.fl.pubchem.xml.ResultTidXML.java Source code

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Here is the source code for edu.scripps.fl.pubchem.xml.ResultTidXML.java

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/*
 * Copyright 2010 The Scripps Research Institute
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
package edu.scripps.fl.pubchem.xml;

import java.util.HashSet;
import java.util.List;
import java.util.Set;

import org.dom4j.Document;
import org.dom4j.Element;
import org.dom4j.Node;

import edu.scripps.fl.pubchem.xml.model.ResultTid;

/*
 * @author S Canny (scanny at scripps dot edu)
 */
public class ResultTidXML {

    public static String rootString = "/PC-AssayContainer/PC-AssaySubmit/PC-AssaySubmit_assay/PC-AssaySubmit_assay_descr/PC-AssayDescription",
            results = "PC-AssayDescription_results";

    public void addTidPlots(Document document, Integer numberPlots) {
        Element root = (Element) document.selectSingleNode(rootString);

        Node dr = root.selectSingleNode("PC-AssayDescription_dr");
        if (dr != null)
            dr.detach();

        Element tidPlotDR = root.addElement("PC-AssayDescription_dr");

        for (int ii = 1; ii <= numberPlots; ii++) {
            Element assayDRAttr = tidPlotDR.addElement("PC-AssayDRAttr");
            assayDRAttr.addElement("PC-AssayDRAttr_id").addText("" + ii);
            assayDRAttr.addElement("PC-AssayDRAttr_descr").addText("Response vs Concentration [" + ii + "]");
            assayDRAttr.addElement("PC-AssayDRAttr_dn").addText("Concentration");
            assayDRAttr.addElement("PC-AssayDRAttr_rn").addText("Response");
        }
    }

    public void buildTidDocument(Document document, List<ResultTid> tidValues) {
        Integer tidInt = decideTids(tidValues);
        if (tidInt > 0) {
            Integer numberPlots = getNumberPlots(tidValues);
            if (numberPlots > 1)
                addTidPlots(document, numberPlots);

            Element root = (Element) document.selectSingleNode(rootString + "/" + results);

            List<Node> nodes = root.selectNodes("PC-ResultType");
            for (Node n : nodes)
                n.detach();

            for (int tt = 0; tt < tidValues.size(); tt++) {
                ResultTid tidValue = tidValues.get(tt);
                Element resultType = root.addElement("PC-ResultType");
                resultType.addElement("PC-ResultType_tid").addText("" + (tt + 1));
                resultType.addElement("PC-ResultType_name").addText(tidValue.getTidName());

                String description = tidValue.getTidDescription();
                if (null != description)
                    resultType.addElement("PC-ResultType_description").addElement("PC-ResultType_description_E")
                            .addText(description);
                String tidType = tidValue.getTidType();
                if (null != tidType)
                    resultType.addElement("PC-ResultType_type").addAttribute("value", tidType)
                            .addText("" + tidValue.getTidTypeValue());
                String tidUnit = tidValue.getTidUnit();
                if (null != tidUnit & "" != tidUnit & tidUnit != "null")
                    resultType.addElement("PC-ResultType_unit").addAttribute("value", tidUnit)
                            .addText("" + tidValue.getTidUnitValue());

                Boolean isAC = tidValue.getIsActiveConcentration();
                if (null != isAC)
                    resultType.addElement("PC-ResultType_ac").addAttribute("value", isAC.toString());

                Double concentration = tidValue.getTidConcentration();
                if (null != concentration) {
                    Element tc = resultType.addElement("PC-ResultType_tc");
                    Element concentrationattr = tc.addElement("PC-ConcentrationAttr");
                    concentrationattr.addElement("PC-ConcentrationAttr_concentration").addText("" + concentration);
                    concentrationattr.addElement("PC-ConcentrationAttr_unit").addAttribute("value", "um")
                            .addText("5");
                    Integer plot = tidValue.getTidPlot();
                    if (null != plot)
                        concentrationattr.addElement("PC-ConcentrationAttr_dr-id").addText("" + plot);
                }
                Integer panelNum = tidValue.getTidPanelNum();
                if (null != panelNum) {
                    Element panel = resultType.addElement("PC-ResultType_panel-info");
                    Element passay = panel.addElement("PC-AssayPanelTestResult");
                    passay.addElement("PC-AssayPanelTestResult_mid").addText("" + panelNum);
                    passay.addElement("PC-AssayPanelTestResult_readout-annot")
                            .addAttribute("value", tidValue.getTidPanelReadout())
                            .addText("" + tidValue.getTidPanelReadoutValue());
                }
            }
        }
    }

    public Integer decideTids(List<ResultTid> tids) {
        Integer tidInt = 0;
        for (int ii = 0; ii <= tids.size() - 1; ii++) {
            ResultTid tid = tids.get(ii);
            if (null != tid.getTidName())
                tidInt = tidInt + 1;
        }
        return tidInt;
    }

    public Integer getNumberPlots(List<ResultTid> tidValues) {
        Set<Integer> plotNumbers = new HashSet<Integer>();

        for (int ii = 0; ii <= tidValues.size() - 1; ii++) {
            ResultTid tidValue = tidValues.get(ii);
            if (null != tidValue.getTidPlot())
                plotNumbers.add(tidValue.getTidPlot());
        }
        Integer numPlots = plotNumbers.size();
        return numPlots;
    }

}