+++ /dev/null
-/*
- * BioJava development code
- *
- * This code may be freely distributed and modified under the
- * terms of the GNU Lesser General Public Licence. This should
- * be distributed with the code. If you do not have a copy,
- * see:
- *
- * http://www.gnu.org/copyleft/lesser.html
- *
- * Copyright for this code is held jointly by the individual
- * authors. These should be listed in @author doc comments.
- *
- * For more information on the BioJava project and its aims,
- * or to join the biojava-l mailing list, visit the home page
- * at:
- *
- * http://www.biojava.org/
- *
- * Created on 19.03.2004
- * @author Andreas Prlic
- *
- */
-package org.biojava.dasobert.das;
-
-import java.util.*;
-
-import org.xml.sax.*;
-import org.xml.sax.helpers.*;
-
-/**
- * a class to parse the response of a DAS - Feature request
- *
- * @author Andreas Prlic Adapted for jalview use.
- * @author Andrew Waterhouse Updated to Das 1.53e feature spec.
- * @author Jim Procter
- *
- */
-public class DAS_Feature_Handler extends DefaultHandler
-{
-
- /**
- *
- */
- List features;
-
- boolean first_flag;
-
- HashMap feature;
-
- String featurefield;
-
- StringBuffer characterdata;
-
- String dasCommand;
-
- int comeBackLater;
-
- int maxFeatures;
-
- String segmentId;
-
- String version;
-
- String type_id;
-
- String type_category;
-
- public DAS_Feature_Handler()
- {
- super();
-
- features = new ArrayList();
- 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;
- }
-
- 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;
- }
-
- public int getMaxFeatures()
- {
- return maxFeatures;
- }
-
- public void setDASCommand(String cmd)
- {
- dasCommand = cmd;
- }
-
- public String getDASCommand()
- {
- return dasCommand;
- }
-
- public List get_features()
- {
- return features;
- }
-
- public int getComBackLater()
- {
- return comeBackLater;
- }
-
- 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 id = atts.getValue("id");
- feature.put("id", id);
- feature.put("dassource", dasCommand);
- characterdata = new StringBuffer();
- }
-
- 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();
- }
-
- 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";
-
- }
-
- 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";
- }
-
- 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");
- }
-
- }
-
- public void startDocument()
- {
- }
-
- public void endDocument()
- {
- }
-
- 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);
- }
- }
- }
-
- 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]);
- }
-
- }
-
-}
git://source.jalview.org / jalview.git / blobdiff