nl.ru.cmbi.vase.web.panel.align.StructurePanel.java Source code

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Here is the source code for nl.ru.cmbi.vase.web.panel.align.StructurePanel.java

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/**
 * Copyright 2014 CMBI (contact: <Coos.Baakman@radboudumc.nl>)
 *
 * 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 nl.ru.cmbi.vase.web.panel.align;

import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;

import nl.ru.cmbi.vase.data.TableData;
import nl.ru.cmbi.vase.data.VASEDataObject;
import nl.ru.cmbi.vase.data.stockholm.Alignment;
import nl.ru.cmbi.vase.data.stockholm.ResidueInfoSet;
import nl.ru.cmbi.vase.tools.util.Utils;
import nl.ru.cmbi.vase.web.page.AlignmentPage;
import nl.ru.cmbi.vase.web.page.HomePage;

import org.apache.wicket.AttributeModifier;
import org.apache.wicket.Component;
import org.apache.wicket.ajax.AbstractDefaultAjaxBehavior;
import org.apache.wicket.ajax.AjaxRequestTarget;
import org.apache.wicket.ajax.markup.html.AjaxFallbackLink;
import org.apache.wicket.core.util.string.JavaScriptUtils;
import org.apache.wicket.markup.html.WebMarkupContainer;
import org.apache.wicket.markup.html.basic.Label;
import org.apache.wicket.markup.html.link.ExternalLink;
import org.apache.wicket.markup.html.list.ListItem;
import org.apache.wicket.markup.html.list.ListView;
import org.apache.wicket.markup.html.panel.Panel;
import org.apache.wicket.model.IModel;
import org.apache.wicket.model.LoadableDetachableModel;
import org.apache.wicket.model.Model;
import org.apache.wicket.request.cycle.RequestCycle;
import org.apache.wicket.request.mapper.parameter.PageParameters;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

public class StructurePanel extends Panel {

    Logger log = LoggerFactory.getLogger(StructurePanel.class);

    public StructurePanel(String id, final String structurePath, final VASEDataObject data) {

        super(id);

        String urlString = RequestCycle.get().urlFor(HomePage.class, new PageParameters()).toString();

        //WebMarkupContainer applet = new WebMarkupContainer("applet");
        //applet.add(new AttributeModifier("codebase",urlString));
        //add(applet);

        final boolean oneChain = Character.isLetter(data.getAlignment().getChainID())
                || Character.isDigit(data.getAlignment().getChainID());

        Component script = new Component("init-script") {

            @Override
            protected void onRender() {

                JavaScriptUtils.writeOpenTag(getResponse());

                getResponse().write("var jmolSelectableAtomColor=\"[126, 193, 255]\";\n");

                getResponse().write("var jmolClearColors=\"");

                if (oneChain) {

                    getResponse().write("select :" + data.getAlignment().getChainID() + " and Protein;");
                    getResponse().write("color \"+ jmolSelectableAtomColor +\";");
                } else {

                    for (Object res : data.getTable().getColumnValues(TableData.pdbResidueID)) {

                        String resString = res.toString().trim();
                        if (resString.isEmpty()) {

                            continue;
                        }

                        getResponse().write("select " + resString + "; color \"+ jmolSelectableAtomColor +\";");
                    }
                }

                getResponse().write("\";\n");

                getResponse().write("var jmolInit=\"");

                getResponse().write("background white;");
                getResponse().write("load " + structurePath + ";");
                getResponse().write("select *;");
                getResponse().write("color atoms lightgrey structure;");

                getResponse().write("\" + jmolClearColors;\n");

                JavaScriptUtils.writeCloseTag(getResponse());
            }
        };
        add(script);
    }
}