updated jalview version of dasobert 1.53e client and added Das Sequence Source discov...

[jalview.git] / src / org / biojava / dasobert / das / DAS_Feature_Handler.java

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 (executable)
--- 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]);
+               }
 
-  }
+       }
 
 }