Team:Freiburg software/Code/BioBrick DAS Feature Handler.java

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/*
/*

Latest revision as of 00:10, 22 October 2009


/*
    Copyright: synbiowave
     
    License: GPL
     
    Authors: Jörg Wassolesk
     
    Version: 0.1 
    
    DESCRIPTION:
    	This class provides the methods for the handling of DAS feature requests.
*/

package org.synbiowave.biobrick;

import org.xml.sax.helpers.DefaultHandler;
import org.xml.sax.Attributes;

import java.util.ArrayList ;
import java.util.HashMap ;
import java.util.List;
import java.util.Map;

// TODO: Auto-generated Javadoc
/**
 * a class to parse the response of a DAS - Feature request.
 * 
 * @author Andreas Prlic
 */
public class BioBrick_DAS_Feature_Handler  extends DefaultHandler{

	/** The features. */
	List<Map<String,String>> features ;
	
	/** The first_flag. */
	boolean first_flag ;
	
	/** The feature. */
	Map<String,String> feature ;
	
	/** The featurefield. */
	String featurefield ;
	
	/** The characterdata. */
	StringBuffer characterdata ;
	
	/** The das command. */
	String dasCommand ;

	/** The come back later. */
	int comeBackLater ;

	/** The max features. */
	int maxFeatures ;

	/** The segment id. */
	String segmentId ;
	
	/** The version. */
	String version;
	
	/** The type_id. */
	String type_id;
	
	/** The type_category. */
	String type_category;
	
	
	/**
	 * Instantiates a new bio brick_ da s_ feature_ handler.
	 */
	public BioBrick_DAS_Feature_Handler() {
		super();

		features= new ArrayList<Map<String, String>>() ;
		first_flag = true ;
		featurefield = "" ;
		characterdata = new StringBuffer();
		dasCommand = "" ;
		comeBackLater = -1; 
		maxFeatures = -1;
		segmentId = "";
		version   = "";
		type_id = "";
		type_category="";
	}

	
	
	/**
	 * get the id information specified int the SEGMENT field of the DAS response.
	 * 
	 * @return the segmentId or an emtpy string if not available
	 */
	public String getSegmentId() {
		return segmentId;
	}

	/**
	 * get the version informationspecified in the SEGMENT field of the DAS response.
	 * 
	 * @return the version information of an empty string if not available
	 */
	public String getVersion() {
		return version;
	}
	
	/**
	 * Checks if is m d5 checksum.
	 * 
	 * @return true, if is m d5 checksum
	 */
	public boolean isMD5Checksum(){
		
		if ((version != null) && (version.length() == 32))
			return true;
		return false;
	}


	/**
	 * specifies a maximum number of features to be downloaded. if a
	 * server returns more, they will be ignored.  default is to load
	 * all features
	 * 
	 * @param max the maximium number of features to be downloaded
	 */

	public void setMaxFeatures(int max) {
		maxFeatures = max;
	}

	/**
	 * Gets the max features.
	 * 
	 * @return the max features
	 */
	public int getMaxFeatures() {
		return maxFeatures;
	}

	/**
	 * Sets the dAS command.
	 * 
	 * @param cmd the new dAS command
	 */
	public void setDASCommand(String cmd) { dasCommand = cmd ;}
	
	/**
	 * Gets the dAS command.
	 * 
	 * @return the dAS command
	 */
	public String getDASCommand() { return dasCommand; }

	/**
	 * Gets the _features.
	 * 
	 * @return the _features
	 */
	public List<Map<String,String>> get_features() {
		return features ;
	}

	/**
	 * Gets the com back later.
	 * 
	 * @return the com back later
	 */
	public int getComBackLater(){
		return comeBackLater;
	}

	/**
	 * Start_feature.
	 * 
	 * @param uri the uri
	 * @param name the name
	 * @param qName the q name
	 * @param atts the atts
	 */
	void start_feature(String uri, String name, String qName, Attributes atts) {

		if (( maxFeatures > 0 ) && ( features.size() > maxFeatures ) ) {
			characterdata = new StringBuffer();
			return;
		}
		feature = new HashMap<String,String>() ;
		String id 	= atts.getValue("id");
		feature.put("id",id);
		feature.put("dassource",dasCommand);
		characterdata = new StringBuffer();
	}

	/**
	 * Add_featuredata.
	 * 
	 * @param uri the uri
	 * @param name the name
	 * @param qName the q name
	 */
	void add_featuredata(String uri, String name, String qName) {
		//System.out.println("featurefield "+featurefield+ " data "+characterdata);
		// NOTE can have multiple lines ..

		if (( maxFeatures > 0 ) && ( features.size() > maxFeatures ) ) {
			return;
		}


		String data = (String)feature.get(featurefield);
		String featureText = characterdata.toString();
		if (data != null){
			featureText = data + " " + featureText;
		}

		if ( qName.equals("TYPE")){
			if ( featureText.length() < 1)
				featureText = type_id;
		
			feature.put("TYPE_ID",type_id);
			feature.put("TYPE_CATEGORY", type_category);
			type_id = "";
			type_category="";
		}
		
		
		feature.put(featurefield,featureText);
		featurefield = "";
		characterdata = new StringBuffer();
	}

	/**
	 * Adds the link.
	 * 
	 * @param uri the uri
	 * @param name the name
	 * @param qName the q name
	 * @param atts the atts
	 */
	private void addLink(String uri, String name, String qName, Attributes atts) {
		String href = atts.getValue("href");
		feature.put("LINK",href);
		characterdata= new StringBuffer();
		featurefield = "LINK-TEXT";

	}

	/**
	 * Adds the group.
	 * 
	 * @param uri the uri
	 * @param name the name
	 * @param qName the q name
	 * @param atts the atts
	 */
	private void addGroup(String uri, String name, String qName, Attributes atts) {
		String id = atts.getValue("id");
		feature.put("GROUP",id);
		characterdata= new StringBuffer();
		featurefield = "GROUP";
	}
	
	/* (non-Javadoc)
	 * @see org.xml.sax.helpers.DefaultHandler#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)
	 */
	public void startElement (String uri, String name, String qName, Attributes atts){
		//System.out.println("new element "+qName);

		if (qName.equals("FEATURE")) 
			start_feature(uri,  name,  qName,  atts);
		else if ( qName.equals("LINK"))
			addLink(uri,name,qName, atts);
		else if ( qName.equals("GROUP"))
			addGroup(uri,name,qName, atts);
		else if ( qName.equals("METHOD") || 
				qName.equals("TYPE") ||
				qName.equals("START") ||
				qName.equals("END") ||
				qName.equals("NOTE") ||                
				qName.equals("SCORE") ||
				qName.equals("ORIENTATION") 				
		){
			characterdata = new StringBuffer();
			featurefield = qName ;
		} else if (qName.equals("SEGMENT")){
			String id = atts.getValue("id");
			if (id != null)
				segmentId = id;
			
			String v = atts.getValue("version");
			if ( v != null)
				version = v;
			
			
		}
		if ( qName.equals("TYPE")){
			type_id      = atts.getValue("id");
			type_category= atts.getValue("category");
		}

	}



	/* (non-Javadoc)
	 * @see org.xml.sax.helpers.DefaultHandler#endElement(java.lang.String, java.lang.String, java.lang.String)
	 */
	public void endElement(String uri, String name, String qName) {

		if ( qName.equals("METHOD") || 
				qName.equals("TYPE") ||
				qName.equals("START") ||
				qName.equals("END") ||
				qName.equals("NOTE") || 
				qName.equals("LINK") || 
				qName.equals("SCORE") ||
				qName.equals("ORIENTATION") ||
				qName.equals("GROUP")
		) {
			add_featuredata(uri,name,qName);
		}
		else if ( qName.equals("FEATURE")) {

			if ( maxFeatures > 0 ) {
				if ( features.size() < maxFeatures ) {
					features.add(feature);
				} 
			} else {
				// no restriction
				features.add(feature);
			}
		}
	}

	/* (non-Javadoc)
	 * @see org.xml.sax.helpers.DefaultHandler#characters(char[], int, int)
	 */
	public void characters (char ch[], int start, int length){
		if ( maxFeatures > 0)
			if ( features.size() > maxFeatures )
				return;

		for (int i = start; i < start + length; i++) {

			characterdata.append(ch[i]);
		}

	}

}