/**
* 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
+public class DAS_Feature_Handler extends DefaultHandler
{
/**
- *
+ *
*/
List features;
+
boolean first_flag;
+
HashMap feature;
+
String featurefield;
- String characterdata;
+
+ 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 = "";
+ characterdata = new StringBuffer();
dasCommand = "";
comeBackLater = -1;
maxFeatures = -1;
+ segmentId = "";
+ version = "";
+ type_id = "";
+ type_category = "";
}
- /** 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
+ /**
+ * 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)
void start_feature(String uri, String name, String qName, Attributes atts)
{
- if ( (maxFeatures > 0) && (features.size() > maxFeatures))
+ if ((maxFeatures > 0) && (features.size() > maxFeatures))
{
- characterdata = "";
+ 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)
{
- //System.out.println("featurefield "+featurefield+ " data "+characterdata);
+ // System.out.println("featurefield "+featurefield+ " data "+characterdata);
// NOTE can have multiple lines ..
- if ( (maxFeatures > 0) && (features.size() > maxFeatures))
+ if ((maxFeatures > 0) && (features.size() > maxFeatures))
{
return;
}
String data = (String) feature.get(featurefield);
+ String featureText = characterdata.toString();
if (data != null)
{
- characterdata = data + " " + characterdata;
+ 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)
+ 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";
}
+ 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)
+ Attributes atts)
{
- //System.out.println("new element "+qName);
+ // System.out.println("new element "+qName);
if (qName.equals("FEATURE"))
{
{
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")
- )
+ 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 = "";
+ 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 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")
- )
+ 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)
{
+ if (maxFeatures > 0)
+ if (features.size() > maxFeatures)
+ return;
for (int i = start; i < start + length; i++)
{
- characterdata += ch[i];
+ characterdata.append(ch[i]);
}
}
git://source.jalview.org / jalview.git / blobdiff