SequencePanel.java

package org.molgenis.mutation.ui.html;

import java.io.Serializable;
import java.util.Formatter;
import java.util.List;

import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang.text.StrBuilder;
import org.molgenis.framework.ui.html.HtmlInput;
import org.molgenis.mutation.dto.ExonDTO;
import org.molgenis.mutation.dto.MutationSummaryDTO;

/*
 * A panel that prints a genomic sequence based on exons and mutations
 */
public class SequencePanel extends HtmlInput<String> implements Serializable
{
	private static final long serialVersionUID = 715300797597319262L;
	private ExonDTO exonDTO;
	private List<MutationSummaryDTO> mutationSummaryDTOList;
	boolean showNuclSequence  = true;
	boolean showAaSequence    = true;
	boolean showBasePositions = true;
	private String baseUrl;

	public SequencePanel(ExonDTO exonDTO, List<MutationSummaryDTO> mutationSummaryDTOList, String baseUrl)
	{
		this.exonDTO                = exonDTO;
		this.mutationSummaryDTOList = mutationSummaryDTOList;
		this.baseUrl                = baseUrl;
	}

	public SequencePanel(String name, String label)
	{
		super(name, label);
		this.setLabel(label);
		this.setClazz("scrollable");
	}

	@Override
	/**
	 * Each input is rendered with a label and in its own div to enable scripting.
	 */
	public String toHtml()
	{
		StrBuilder result = new StrBuilder();

		result.appendln("<div class=\"" + this.getClazz() + "\">");
		result.appendln("<pre>");

		if (this.showNuclSequence)
		{
			result.append(this.exonDTO.getNuclSequenceFlankLeft());
			result.append("<span class=\"seq\">");
			int startPos = this.exonDTO.getGdnaStart();
			int endPos = this.exonDTO.getGdnaEnd();
			for (int i = startPos; ("R".equals(this.exonDTO.getOrientation()) ? i >= endPos : i <= endPos); i = ("R"
					.equals(this.exonDTO.getOrientation()) ? i - 1 : i + 1))
			{
				// System.out.println(">>> SequencePanel: seqlen==" +
				// exonDTO.getNuclSequence().length() + ", startPos==" +
				// startPos + ", i==" + i);
				boolean hasMutation = false;
				for (MutationSummaryDTO mutationSummaryVO : this.mutationSummaryDTOList)
				{
					// System.out.println(">>> SequencePanel: m.cdna==" +
					// mutationSummaryVO.getCdnaNotation() + ", m.gdna=" +
					// mutationSummaryVO.getGdnaNotation());
					String url = this.baseUrl;
					url = StringUtils.replace(url, "mid=", "mid=" + mutationSummaryVO.getIdentifier());
					String tooltip = mutationSummaryVO.getNiceNotation();
					if (mutationSummaryVO.getGdnaStart() == i)
					{
						hasMutation = true;
						result.append("<span class=\"mut\">");
						result.append("<a class=\"mut\" href=\"" + url + "\" alt=\"" + tooltip + "\" title=\""
								+ tooltip + "\">");
						break;
					}
				}
				if (StringUtils.equals(this.exonDTO.getOrientation(), "R")) result.append(this.exonDTO
						.getNuclSequence().substring(startPos - i, startPos - i + 1)); // ${exonSummaryVO.nuclSequence?substring(exonSummaryVO.exon.getGdna_Position()
																						// -
																						// i,
																						// exonSummaryVO.exon.getGdna_Position()
																						// -
																						// i
																						// +
																						// 1)}
				else if (StringUtils.equals(this.exonDTO.getOrientation(), "F")) result.append(this.exonDTO
						.getNuclSequence().substring(i - startPos, i - startPos + 1));

				if (hasMutation)
				{
					result.append("</a></span>");
				}
			}
			result.append("</span>");
			result.appendln(this.exonDTO.getNuclSequenceFlankRight());
		}

		if (!this.exonDTO.getIsIntron())
		{
			// print aa sequence
			if (this.showAaSequence)
			{
				result.appendPadding(this.exonDTO.getNuclSequenceFlankLeft().length(), ' ');
				result.append("<span class=\"seq\">");
				result.append(this.exonDTO.getAaSequence());
				result.appendln("</span>");
			}

			// print base numbers
			if (this.showBasePositions)
			{
				result.appendPadding(this.exonDTO.getNuclSequenceFlankLeft().length(), ' ');
				result.append("<span>");
				result.append(this.printBasePositions(this.exonDTO));
				result.appendln("</span>");
			}
		}

		result.appendln("</pre>\n");
		result.appendln("</div>\n");

		return result.toString();
	}

	public void setShowNuclSequence(boolean showNuclSequence)
	{
		this.showNuclSequence = showNuclSequence;
	}

	public void setShowAaSequence(boolean showAaSequence)
	{
		this.showAaSequence = showAaSequence;
	}

	public void setShowBasePositions(boolean showBasePositions)
	{
		this.showBasePositions = showBasePositions;
	}

	public void setBaseUrl(String baseUrl)
	{
		this.baseUrl = baseUrl;
	}

	private String printBasePositions(ExonDTO exonSummaryVO)
	{
		// <#list exon.cdna_position..exon.cdna_position + exon.length as i>
		StringBuffer buf = new StringBuffer();

		for (int i = exonSummaryVO.getCdnaStart(); i < exonSummaryVO.getCdnaEnd(); i++)
			if (i % 10 == 0) buf.append(new Formatter().format("%4s", i).toString());
			else if (i % 10 < 7) // (i % 10 > 3 || i < 4)
			buf.append(" "); // new Integer(i % 10).toString(); //" ";
		// else
		// return "";
		return buf.toString();
	}
}