Merge branch 'develop' into bug/JAL-2255_seq-fetcher-broken-on-linux

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

diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index ddb2ddc..fd971fd 100755 (executable)
--- a/src/jalview/io/JPredFile.java
+++ b/src/jalview/io/JPredFile.java
@@ -70,15 +70,16 @@ public class JPredFile extends AlignFile
    * 
    * @param inFile
    *          DOCUMENT ME!
-   * @param type
+   * @param sourceType
    *          DOCUMENT ME!
    * 
    * @throws IOException
    *           DOCUMENT ME!
    */
-  public JPredFile(String inFile, String type) throws IOException
+  public JPredFile(String inFile, DataSourceType sourceType)
+          throws IOException
   {
-    super(inFile, type);
+    super(inFile, sourceType);
   }
 
   public JPredFile(FileParse source) throws IOException
@@ -130,6 +131,7 @@ public class JPredFile extends AlignFile
   /**
    * DOCUMENT ME!
    */
+  @Override
   public void initData()
   {
     super.initData();
@@ -141,6 +143,7 @@ public class JPredFile extends AlignFile
   /**
    * parse a JPred concise file into a sequence-alignment like object.
    */
+  @Override
   public void parse() throws IOException
   {
     // JBPNote log.System.out.println("all read in ");
@@ -205,7 +208,7 @@ public class JPredFile extends AlignFile
             ascore = symbols.nextToken();
 
             Float score = new Float(ascore);
-            scores.addElement((Object) score);
+            scores.addElement(score);
           }
 
           Scores.put(id, scores);
@@ -217,15 +220,15 @@ public class JPredFile extends AlignFile
           for (int j = 0; j < i; j++)
           {
             scores.setElementAt(
-                    (Object) ((Float) scores.elementAt(j)).toString(), j);
+                    ((Float) scores.elementAt(j)).toString(), j);
           }
 
-          scores.addElement((Object) ascore);
+          scores.addElement(ascore);
 
           while (symbols.hasMoreTokens())
           {
             ascore = symbols.nextToken();
-            scores.addElement((Object) ascore);
+            scores.addElement(ascore);
           }
 
           Scores.put(id, scores);
@@ -265,7 +268,9 @@ public class JPredFile extends AlignFile
           }
 
           if (QuerySeqPosition == -1)
+          {
             QuerySeqPosition = ids.size();
+          }
           ids.addElement(name);
           noSeqs++;
         }
@@ -278,7 +283,7 @@ public class JPredFile extends AlignFile
 
           seq_entries.addElement(newseq.toString());
           ids.addElement(id);
-          Symscores.put((Object) id, (Object) new Integer(ids.size() - 1));
+          Symscores.put(id, new Integer(ids.size() - 1));
         }
       }
     }
@@ -350,7 +355,8 @@ public class JPredFile extends AlignFile
    * 
    * @return String
    */
-  public String print()
+  @Override
+  public String print(SequenceI[] sqs, boolean jvsuffix)
   {
     return "Not Supported";
   }
@@ -365,13 +371,13 @@ public class JPredFile extends AlignFile
   {
     try
     {
-      JPredFile blc = new JPredFile(args[0], "File");
+      JPredFile jpred = new JPredFile(args[0], DataSourceType.FILE);
 
-      for (int i = 0; i < blc.seqs.size(); i++)
+      for (int i = 0; i < jpred.seqs.size(); i++)
       {
-        System.out.println(((Sequence) blc.seqs.elementAt(i)).getName()
+        System.out.println(((Sequence) jpred.seqs.elementAt(i)).getName()
                 + "\n"
-                + ((Sequence) blc.seqs.elementAt(i)).getSequenceAsString()
+                + ((Sequence) jpred.seqs.elementAt(i)).getSequenceAsString()
                 + "\n");
       }
     } catch (java.io.IOException e)
@@ -402,7 +408,7 @@ public class JPredFile extends AlignFile
     }
     // check that no stray annotations have been added at the end.
     {
-      SequenceI sq = (SequenceI) seqs.elementAt(j - 1);
+      SequenceI sq = seqs.elementAt(j - 1);
       if (sq.getName().toUpperCase().startsWith("JPRED"))
       {
         annotSeqs.addElement(sq);