X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Forg%2Fbiojava%2Fdasobert%2Fdas%2FDAS_Feature_Handler.java;h=eed54e8ceb2039c8f9fd336d491953fa999eecd8;hb=54e003f9b2fff47dbfea6401c3944afdb7bd37b3;hp=b506c513377e4902e84c49fddc13a5a197d8f465;hpb=b318e1301843732eabd1b34ce391828887c883df;p=jalview.git

diff --git a/src/org/biojava/dasobert/das/DAS_Feature_Handler.java b/src/org/biojava/dasobert/das/DAS_Feature_Handler.java
index b506c51..eed54e8 100755
--- a/src/org/biojava/dasobert/das/DAS_Feature_Handler.java
+++ b/src/org/biojava/dasobert/das/DAS_Feature_Handler.java
@@ -31,7 +31,11 @@ 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
@@ -44,25 +48,60 @@ public class DAS_Feature_Handler
   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
@@ -103,16 +142,15 @@ public class DAS_Feature_Handler
   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)
@@ -126,28 +164,44 @@ public class DAS_Feature_Handler
     }
 
     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"))
@@ -157,18 +211,32 @@ public class DAS_Feature_Handler
     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");
+		}
 
   }
 
@@ -189,9 +257,10 @@ public class DAS_Feature_Handler
         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"))
@@ -212,15 +281,16 @@ public class DAS_Feature_Handler
     }
   }
 
-  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]);
+		}
 
-  }
+	}
 
 }