*/
package org.biojava.dasobert.das;
-import org.xml.sax.helpers.DefaultHandler;
-import org.xml.sax.Attributes;
+import java.util.*;
-import java.util.ArrayList ;
-import java.util.HashMap ;
-import java.util.List;
+import org.xml.sax.*;
+import org.xml.sax.helpers.*;
/**
* a class to parse the response of a DAS - Feature request
- * @author Andreas Prlic
- *
+ *
+ * @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 ;
- String characterdata ;
- String dasCommand ;
-
- int comeBackLater ;
-
- public DAS_Feature_Handler() {
- super();
-
- features= new ArrayList() ;
- first_flag = true ;
- featurefield = "" ;
- characterdata = "";
- dasCommand = "" ;
- comeBackLater = -1;
+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;
}
-
- public void setDASCommand(String cmd) { dasCommand = cmd ;}
- public String getDASCommand() { return dasCommand; }
-
- public List get_features() {
- return features ;
+ 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;
}
-
- public int getComBackLater(){
- return comeBackLater;
+
+ String data = (String) feature.get(featurefield);
+ String featureText = characterdata.toString();
+ if (data != null)
+ {
+ featureText = data + " " + featureText;
}
-
- void start_feature(String uri, String name, String qName, Attributes atts) {
- feature = new HashMap() ;
- String id = atts.getValue("id");
- feature.put("id",id);
- feature.put("dassource",dasCommand);
- characterdata = "";
+
+ 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 = "";
}
-
- void add_featuredata(String uri, String name, String qName) {
- //System.out.println("featurefield "+featurefield+ " data "+characterdata);
- // NOTE can have multiple lines ..
-
- String data = (String)feature.get(featurefield);
- if (data != null){
- characterdata = data + " " + characterdata;
- }
-
- feature.put(featurefield,characterdata);
- featurefield = "";
- characterdata = "";
+
+ 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);
}
-
- private void addLink(String uri, String name, String qName, Attributes atts) {
- String href = atts.getValue("href");
- feature.put("LINK",href);
- characterdata="";
- featurefield = "LINK-TEXT";
-
+ else if (qName.equals("LINK"))
+ {
+ addLink(uri, name, qName, atts);
}
-
- 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("METHOD") ||
- qName.equals("TYPE") ||
- qName.equals("START") ||
- qName.equals("END") ||
- qName.equals("NOTE") ||
- qName.equals("SCORE")
- ){
- characterdata ="";
- featurefield = qName ;
- }
-
+ else if (qName.equals("GROUP"))
+ {
+ addGroup(uri, name, qName, atts);
}
-
- public void startDocument() {
- //System.out.println("start document");
+ 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;
}
-
- public void endDocument () {
- //System.out.println("adding feature " + feature);
- //features.add(feature);
-
+ 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;
+
}
- public void endElement(String uri, String name, String qName) {
- //System.out.println("end "+name);
- if ( qName.equals("METHOD") ||
- qName.equals("TYPE") ||
- qName.equals("START") ||
- qName.equals("END") ||
- qName.equals("NOTE") ||
- qName.equals("LINK") ||
- qName.equals("SCORE")
- ) {
- add_featuredata(uri,name,qName);
- }
- else if ( qName.equals("FEATURE")) {
- //System.out.println("adding ffeature " + feature);
- features.add(feature);
- }
+ 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);
}
-
- public void characters (char ch[], int start, int length){
- //System.out.println("characters");
- for (int i = start; i < start + length; i++) {
-
- characterdata += ch[i];
+ 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