JAL-1551 formatting

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 5d645ca..a3f7531 100644 (file)
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -219,7 +219,7 @@ public class StockholmFile extends AlignFile
     if (!r.search(nextLine()))
     {
       throw new IOException(MessageManager
-              .getString("exception.stockholm_invalid_format"));
+                           .getString("exception.stockholm_invalid_format") +" ("+r+")");
     }
     else
     {

diff --git a/src/jalview/ws/dbsources/Pfam.java b/src/jalview/ws/dbsources/Pfam.java
index 0c21d42..93001a4 100644 (file)
--- a/src/jalview/ws/dbsources/Pfam.java
+++ b/src/jalview/ws/dbsources/Pfam.java
@@ -22,12 +22,12 @@ package jalview.ws.dbsources;
 
 import java.util.Locale;
 
+import com.stevesoft.pat.Regex;
+
 import jalview.bin.Cache;
 import jalview.datamodel.DBRefSource;
 import jalview.util.Platform;
 
-import com.stevesoft.pat.Regex;
-
 /**
  * TODO: later PFAM is a complex datasource - it could return a tree in addition
  * to an alignment TODO: create interface to pass alignment properties and tree
@@ -38,17 +38,21 @@ import com.stevesoft.pat.Regex;
  */
 abstract public class Pfam extends Xfam
 {
-    public static final String FULL="full",RP35="rp35",RP15="rp15",RP75="rp75",RP55="rp55",SEED="seed";
-       
-   public String getPfamDownloadURL(String id,String alType) {
-       String url = Cache.getDefault(PFAM_BASEURL_KEY,DEFAULT_PFAM_BASEURL);
-       url = url.replace("$PFAMID$",id);
-       url = url.replace("$ALTYPE$",alType);
-       return url;
-    }
+  public static final String FULL = "full", RP35 = "rp35", RP15 = "rp15",
+          RP75 = "rp75", RP55 = "rp55", SEED = "seed";
+
+  public String getPfamDownloadURL(String id, String alType)
+  {
+    String url = Cache.getDefault(PFAM_BASEURL_KEY, DEFAULT_PFAM_BASEURL);
+    url = url.replace("$PFAMID$", id);
+    url = url.replace("$ALTYPE$", alType);
+    return url;
+  }
+
   static final String PFAM_BASEURL_KEY = "PFAM_INTERPRO_URL_TEMPLATE";
 
   protected String alignmentType;
+
   private static final String DEFAULT_PFAM_BASEURL = "https://www.ebi.ac.uk/interpro/wwwapi/entry/pfam/$PFAMID$/?annotation=alignment:$ALTYPE$&download";
 
   static
@@ -61,11 +65,11 @@ abstract public class Pfam extends Xfam
     super();
   }
 
-    
-    String getURL(String queries)
+  @Override
+  String getURL(String queries)
   {
-      return getPfamDownloadURL(
-                                queries.trim().toUpperCase(Locale.ROOT), alignmentType);
+    return getPfamDownloadURL(queries.trim().toUpperCase(Locale.ROOT),
+            alignmentType);
   }
 
   /*

diff --git a/src/jalview/ws/dbsources/PfamFull.java b/src/jalview/ws/dbsources/PfamFull.java
index ffb5e41..6cf5fda 100644 (file)
--- a/src/jalview/ws/dbsources/PfamFull.java
+++ b/src/jalview/ws/dbsources/PfamFull.java
@@ -29,7 +29,7 @@ public class PfamFull extends Pfam
   public PfamFull()
   {
     super();
-    alignmentType=FULL;
+    alignmentType = FULL;
   }
 
   /*

diff --git a/src/jalview/ws/dbsources/PfamSeed.java b/src/jalview/ws/dbsources/PfamSeed.java
index 6d486e8..45a1840 100644 (file)
--- a/src/jalview/ws/dbsources/PfamSeed.java
+++ b/src/jalview/ws/dbsources/PfamSeed.java
@@ -31,7 +31,7 @@ public class PfamSeed extends Pfam
   public PfamSeed()
   {
     super();
-    alignmentType=SEED;
+    alignmentType = SEED;
   }
 
   /*

diff --git a/test/jalview/ws/dbsources/PfamFullTest.java b/test/jalview/ws/dbsources/PfamFullTest.java
index eb2f147..fd59ef3 100644 (file)
--- a/test/jalview/ws/dbsources/PfamFullTest.java
+++ b/test/jalview/ws/dbsources/PfamFullTest.java
@@ -22,11 +22,11 @@ package jalview.ws.dbsources;
 
 import static org.testng.Assert.assertEquals;
 
-import jalview.bin.Cache;
-
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
+import jalview.bin.Cache;
+
 public class PfamFullTest
 {
   @BeforeClass(alwaysRun = true)
@@ -38,14 +38,15 @@ public class PfamFullTest
   @Test(groups = "Functional")
   public void testGetURL()
   {
-      String path = "www.ebi.ac.uk/interpro/wwwapi/entry/pfam/ABC/?annotation=alignment:full&download";
+    String path = "www.ebi.ac.uk/interpro/wwwapi/entry/pfam/ABC/?annotation=alignment:full&download";
 
     // with default value for domain
     String url = new PfamFull().getURL(" abc ");
     assertEquals(url, "https://" + path);
 
     // with override in properties
-    Cache.setProperty(Pfam.PFAM_BASEURL_KEY, "http://www.ebi.ac.uk/interpro/wwwapi/entry/pfam/$PFAMID$/?annotation=alignment:$ALTYPE$&download");
+    Cache.setProperty(Pfam.PFAM_BASEURL_KEY,
+            "http://www.ebi.ac.uk/interpro/wwwapi/entry/pfam/$PFAMID$/?annotation=alignment:$ALTYPE$&download");
     url = new PfamFull().getURL(" abc ");
     assertEquals(url, "http://" + path);
   }

diff --git a/test/jalview/ws/dbsources/PfamSeedTest.java b/test/jalview/ws/dbsources/PfamSeedTest.java
index 451810b..d228c35 100644 (file)
--- a/test/jalview/ws/dbsources/PfamSeedTest.java
+++ b/test/jalview/ws/dbsources/PfamSeedTest.java
@@ -22,11 +22,11 @@ package jalview.ws.dbsources;
 
 import static org.testng.Assert.assertEquals;
 
-import jalview.bin.Cache;
-
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
+import jalview.bin.Cache;
+
 public class PfamSeedTest
 {
   @BeforeClass(alwaysRun = true)
@@ -38,14 +38,15 @@ public class PfamSeedTest
   @Test(groups = "Functional")
   public void testGetURL()
   {
-    String path = "pfam.xfam.org/family/ABC/alignment/seed/gzipped";
+    String path = "www.ebi.ac.uk/interpro/wwwapi/entry/pfam/ABC/?annotation=alignment:seed&download";
 
     // with default value for domain
     String url = new PfamSeed().getURL(" abc ");
     assertEquals(url, "https://" + path);
 
     // with override in properties
-    Cache.setProperty(Pfam.PFAM_BASEURL_KEY, "http://pfam.xfam.org");
+    Cache.setProperty(Pfam.PFAM_BASEURL_KEY,
+            "http://www.ebi.ac.uk/interpro/wwwapi/entry/pfam/$PFAMID$/?annotation=alignment:$ALTYPE$&download");
     url = new PfamSeed().getURL(" abc ");
     assertEquals(url, "http://" + path);
   }