Merge branch 'features/JAL-2040_JAL-2137_phyre2' into reviews/features/JAL-2136_phyre...

[jalview.git] / src / jalview / io / AnnotationFile.java

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index eca27a7..2491464 100755 (executable)
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -665,7 +665,7 @@ public class AnnotationFile
   String refSeqId = null;
 
   public boolean annotateAlignmentView(AlignViewportI viewport,
-          String file, String protocol)
+          String file, DataSourceType protocol)
   {
     ColumnSelection colSel = viewport.getColumnSelection();
     if (colSel == null)
@@ -683,19 +683,19 @@ public class AnnotationFile
   }
 
   public boolean readAnnotationFile(AlignmentI al, String file,
-          String protocol)
+          DataSourceType sourceType)
   {
-    return readAnnotationFile(al, null, file, protocol);
+    return readAnnotationFile(al, null, file, sourceType);
   }
 
   public boolean readAnnotationFile(AlignmentI al, ColumnSelection colSel,
-          String file, String protocol)
+          String file, DataSourceType sourceType)
   {
     baseUri = "";
     BufferedReader in = null;
     try
     {
-      if (protocol.equals(AppletFormatAdapter.FILE))
+      if (sourceType == DataSourceType.FILE)
       {
         in = new BufferedReader(new FileReader(file));
         baseUri = new File(file).getParent();
@@ -708,7 +708,7 @@ public class AnnotationFile
           baseUri += "/";
         }
       }
-      else if (protocol.equals(AppletFormatAdapter.URL))
+      else if (sourceType == DataSourceType.URL)
       {
         URL url = new URL(file);
         in = new BufferedReader(new InputStreamReader(url.openStream()));
@@ -721,13 +721,13 @@ public class AnnotationFile
           baseUri = baseUri.substring(0, baseUri.lastIndexOf("/")) + "/";
         }
       }
-      else if (protocol.equals(AppletFormatAdapter.PASTE))
+      else if (sourceType == DataSourceType.PASTE)
       {
         in = new BufferedReader(new StringReader(file));
         // TODO - support mimencoded PDBs for a paste.. ?
         baseUri = "";
       }
-      else if (protocol.equals(AppletFormatAdapter.CLASSLOADER))
+      else if (sourceType == DataSourceType.CLASSLOADER)
       {
         java.io.InputStream is = getClass().getResourceAsStream("/" + file);
         if (is != null)
@@ -1808,9 +1808,8 @@ public class AnnotationFile
         else if (key.equalsIgnoreCase("consThreshold"))
         {
           sg.cs.setConservationInc(Integer.parseInt(value));
-          Conservation c = new Conservation("Group", 3,
-                  sg.getSequences(null), sg.getStartRes(),
-                  sg.getEndRes() + 1);
+          Conservation c = new Conservation("Group", sg.getSequences(null),
+                  sg.getStartRes(), sg.getEndRes() + 1);
 
           c.calculate();
           c.verdict(false, 25); // TODO: refer to conservation percent threshold