/**
* 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 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;
+
StringBuffer characterdata;
+
String dasCommand;
int comeBackLater;
int maxFeatures;
- String segmentId ;
- String version;
- String type_id;
- String type_category;
-
-
- 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 = new StringBuffer();
+ 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;
+ 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;
}
-
- public boolean isMD5Checksum(){
- if ((version != null) && (version.length() == 32))
- return true;
- return false;
- }
+ /**
+ * 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
+ /**
+ * 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 ) ) {
- characterdata = new StringBuffer();
+ 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();
+ 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){
- featureText = data + " " + featureText;
+ 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);
+ 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();
+ 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= new StringBuffer();
+ 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);
+ 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") ||
- qName.equals("ORIENTATION")
- ){
+ }
+ 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");
- }
+ }
+ 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") ||
- qName.equals("ORIENTATION") ||
- qName.equals("GROUP")
- ) {
+ 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"))
}
}
- public void characters (char ch[], int start, int length){
- if ( maxFeatures > 0)
- if ( features.size() > maxFeatures )
- return;
+ 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.append(ch[i]);
- }
+ characterdata.append(ch[i]);
+ }
- }
+ }
}
git://source.jalview.org / jalview.git / blobdiff