Modified example query string for different Intermine descendants

diff --git a/src/jalview/ws/HttpClientUtils.java b/src/jalview/ws/HttpClientUtils.java
index 4b6129f..dccf19b 100644 (file)
--- a/src/jalview/ws/HttpClientUtils.java
+++ b/src/jalview/ws/HttpClientUtils.java
@@ -89,11 +89,10 @@ public class HttpClientUtils
   {
     HttpClient httpclient = new DefaultHttpClient();
     HttpGet httpget = new HttpGet(getUrl);
-    // httpget.setParams(params);
+    String responseString = "";
     HttpResponse response = httpclient.execute(httpget);
     HttpEntity resEntity = response.getEntity();
 
-
     if (resEntity != null)
     {
       BufferedReader r = new BufferedReader(new InputStreamReader(
@@ -105,12 +104,9 @@ public class HttpClientUtils
       {
         responseBuilder.append(aux);
       }
-      return responseBuilder.toString();
-    }
-    else
-    {
-      return null;
+      responseString = responseBuilder.toString();
     }
+    return responseString;
   }
 
   public static BufferedReader doHttpMpartFilePost(String postUrl,

diff --git a/src/jalview/ws/dbsources/FlyMine.java b/src/jalview/ws/dbsources/FlyMine.java
index d597608..99bf4fb 100644 (file)
--- a/src/jalview/ws/dbsources/FlyMine.java
+++ b/src/jalview/ws/dbsources/FlyMine.java
@@ -9,14 +9,13 @@ public class FlyMine extends Intermine
     this.name = "FlyMine";
     this.baseUrl = "http://www.flymine.org/query";
     this.domain = "7227";
-    this.testQuery = "2L";
+    this.testQuery = "2L:1-500";
   }
 
   @Override
   public AlignmentI getSequenceRecords(String queries) throws Exception
   {
-    return getAlignmentData(baseUrl, queries, domain, seqStart,
-            seqEnd);
+    return getAlignmentData(baseUrl, queries, domain);
   }
 
 }

diff --git a/src/jalview/ws/dbsources/Intermine.java b/src/jalview/ws/dbsources/Intermine.java
index d319c50..7863409 100644 (file)
--- a/src/jalview/ws/dbsources/Intermine.java
+++ b/src/jalview/ws/dbsources/Intermine.java
@@ -29,7 +29,7 @@ public abstract class Intermine extends DbSourceProxyImpl
 
   protected String baseUrl = "";
 
-  protected String testQuery = "";
+  protected String testQuery = "seqRef:start-end";
 
   @Override
   public String getDbSource()
@@ -76,7 +76,7 @@ public abstract class Intermine extends DbSourceProxyImpl
 
   @SuppressWarnings("unchecked")
   public Alignment getAlignmentData(String baseUrl, String query,
-          String domain, int seqStart, int seqEnd)
+          String domain)
   {
 
     StringTokenizer queries = new StringTokenizer(query, ";");
@@ -89,7 +89,6 @@ public abstract class Intermine extends DbSourceProxyImpl
       {
         String uniquequery = queries.nextToken();
         String seqRef = uniquequery;
-        // StringTokenizer queryParam = new StringTokenizer(uniquequery, ":");
         String[] queryParam = uniquequery.split(":");
         if (queryParam.length > 1)
         {
@@ -107,13 +106,14 @@ public abstract class Intermine extends DbSourceProxyImpl
                 seqRef, domain,
                 seqStart, seqEnd, true);
         String rawAnnotationData = fetchData(baseUrl,
-                uniquequery, domain, seqStart, seqEnd, false);
+ seqRef, domain,
+                seqStart, seqEnd, false);
         stopQuery();
 
         String sequenceString = "";
 
-        // System.out.println("Sequence data: " + rawSequenceData);
-        // System.out.println("Annotation data : " + rawAnnotationData);
+        System.out.println("Sequence data: " + rawSequenceData);
+        System.out.println("Annotation data : " + rawAnnotationData);
         JSONParser jsonParser = new JSONParser();
         JSONObject rawSeqJson = (JSONObject) jsonParser
                 .parse(rawSequenceData);
@@ -129,7 +129,7 @@ public abstract class Intermine extends DbSourceProxyImpl
           int start = Integer.valueOf(feature.get("start").toString());
           int end = Integer.valueOf(feature.get("end").toString());
 
-          retrievedSeq[count++] = new Sequence(uniquequery, sequenceString,
+          retrievedSeq[count++] = new Sequence(seqRef, sequenceString,
                   start,
                   end);
         }
@@ -148,7 +148,8 @@ public abstract class Intermine extends DbSourceProxyImpl
   {
     String resourceUrl = baseUrl + "/service/jbrowse/" + domain
             + "/features/" + seqRef + "?start=" + start + "&end=" + end
-            + "&reference=" + fetchRef;
+            + ((fetchRef) ? "&reference=true" : "");
+    System.out.println("resource url : " + resourceUrl);
     return HttpClientUtils.doHttpUrlGet(resourceUrl);
   }
 

diff --git a/src/jalview/ws/dbsources/ModMine.java b/src/jalview/ws/dbsources/ModMine.java
index c8c0d0d..d521f16 100644 (file)
--- a/src/jalview/ws/dbsources/ModMine.java
+++ b/src/jalview/ws/dbsources/ModMine.java
@@ -9,13 +9,13 @@ public class ModMine extends Intermine
     this.name = "ModMine";
     this.baseUrl = "http://intermine.modencode.org/modminetest";
     this.domain = "7227";
-    this.testQuery = "2L";
+    this.testQuery = "2L:1-500";
   }
 
   @Override
   public AlignmentI getSequenceRecords(String queries) throws Exception
   {
-    return getAlignmentData(baseUrl, queries, domain, seqStart, seqEnd);
+    return getAlignmentData(baseUrl, queries, domain);
   }
 
 }

diff --git a/src/jalview/ws/dbsources/MouseMine.java b/src/jalview/ws/dbsources/MouseMine.java
index 15306c1..409ec17 100644 (file)
--- a/src/jalview/ws/dbsources/MouseMine.java
+++ b/src/jalview/ws/dbsources/MouseMine.java
@@ -15,7 +15,7 @@ public class MouseMine extends Intermine
   @Override
   public AlignmentI getSequenceRecords(String queries) throws Exception
   {
-    return getAlignmentData(baseUrl, queries, domain, seqStart, seqEnd);
+    return getAlignmentData(baseUrl, queries, domain);
   }
 
 }

diff --git a/src/jalview/ws/dbsources/RatMine.java b/src/jalview/ws/dbsources/RatMine.java
index 25dfb46..0fcfd3a 100644 (file)
--- a/src/jalview/ws/dbsources/RatMine.java
+++ b/src/jalview/ws/dbsources/RatMine.java
@@ -16,7 +16,7 @@ public class RatMine extends Intermine
   @Override
   public AlignmentI getSequenceRecords(String queries) throws Exception
   {
-    return getAlignmentData(baseUrl, queries, domain, seqStart, seqEnd);
+    return getAlignmentData(baseUrl, queries, domain);
   }
 
 }

diff --git a/src/jalview/ws/dbsources/YeastMine.java b/src/jalview/ws/dbsources/YeastMine.java
index 15fa8fe..a01fa72 100644 (file)
--- a/src/jalview/ws/dbsources/YeastMine.java
+++ b/src/jalview/ws/dbsources/YeastMine.java
@@ -9,13 +9,13 @@ public class YeastMine extends Intermine
     this.name = "YeastMine";
     this.baseUrl = "http://yeastmine.yeastgenome.org/yeastmine";
     this.domain = "4932";
-    this.testQuery = "chrI";
+    this.testQuery = "chrI:1-500";
   }
 
   @Override
   public AlignmentI getSequenceRecords(String queries) throws Exception
   {
-    return getAlignmentData(baseUrl, queries, domain, seqStart, seqEnd);
+    return getAlignmentData(baseUrl, queries, domain);
   }