/**
* 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
boolean first_flag;
HashMap feature;
String featurefield;
- String characterdata;
+ StringBuffer characterdata;
String dasCommand;
int comeBackLater;
int maxFeatures;
- public DAS_Feature_Handler()
- {
+ String segmentId ;
+ String version;
+ String type_id;
+ String type_category;
+
+
+ public DAS_Feature_Handler() {
super();
features = new ArrayList();
first_flag = true;
featurefield = "";
- characterdata = "";
+ 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
void start_feature(String uri, String name, String qName, Attributes atts)
{
- if ( (maxFeatures > 0) && (features.size() > maxFeatures))
- {
- characterdata = "";
+ 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 = "";
+ characterdata = new StringBuffer();
}
void add_featuredata(String uri, String name, String qName)
}
String data = (String) feature.get(featurefield);
- if (data != null)
- {
- characterdata = data + " " + characterdata;
+ String featureText = characterdata.toString();
+ if (data != null){
+ featureText = data + " " + featureText;
}
- feature.put(featurefield, 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="";
+ }
+
+
+ feature.put(featurefield,featureText);
featurefield = "";
- characterdata = "";
+ characterdata = new StringBuffer();
}
private void addLink(String uri, String name, String qName, Attributes atts)
{
String href = atts.getValue("href");
feature.put("LINK", href);
- characterdata = "";
+ characterdata= new StringBuffer();
featurefield = "LINK-TEXT";
}
- public void startElement(String uri, String name, String qName,
- Attributes 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";
+ }
+
+ public void startElement (String uri, String name, String qName, Attributes atts){
//System.out.println("new element "+qName);
if (qName.equals("FEATURE"))
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")
- )
- {
- characterdata = "";
+ 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");
+ }
}
qName.equals("END") ||
qName.equals("NOTE") ||
qName.equals("LINK") ||
- qName.equals("SCORE")
- )
- {
+ qName.equals("SCORE") ||
+ qName.equals("ORIENTATION") ||
+ qName.equals("GROUP")
+ ) {
add_featuredata(uri, name, qName);
}
else if (qName.equals("FEATURE"))
}
}
- public void characters(char ch[], int start, int length)
- {
+ 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++)
- {
+ for (int i = start; i < start + length; i++) {
- characterdata += ch[i];
- }
+ characterdata.append(ch[i]);
+ }
- }
+ }
}