X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJPredFile.java;h=e375df7c19e307b79efc5f087c6ad6c7f4f9fa20;hb=a83adb45bdf9554e270921b4baad94defd314b36;hp=abd44c09da8f81e2a45dc1748e876ab7fe90f8a5;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git

diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index abd44c0..e375df7 100755
--- a/src/jalview/io/JPredFile.java
+++ b/src/jalview/io/JPredFile.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -25,12 +25,17 @@
  */
 package jalview.io;
 
-import java.io.*;
-import java.util.*;
-
-import jalview.datamodel.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
 import jalview.util.MessageManager;
 
+import java.io.IOException;
+import java.util.Hashtable;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
 /**
  * Parser for the JPred/JNet concise format. This is a series of CSV lines, each
  * line is either a sequence (QUERY), a sequence profile (align;), or jnet
@@ -63,17 +68,20 @@ public class JPredFile extends AlignFile
   /**
    * Creates a new JPredFile object.
    * 
+   * BH allows File or String
+   * 
    * @param inFile
    *          DOCUMENT ME!
-   * @param type
+   * @param sourceType
    *          DOCUMENT ME!
    * 
    * @throws IOException
    *           DOCUMENT ME!
    */
-  public JPredFile(String inFile, String type) throws IOException
+  public JPredFile(Object inFile, DataSourceType sourceType)
+          throws IOException
   {
-    super(inFile, type);
+    super(inFile, sourceType);
   }
 
   public JPredFile(FileParse source) throws IOException
@@ -125,6 +133,7 @@ public class JPredFile extends AlignFile
   /**
    * DOCUMENT ME!
    */
+  @Override
   public void initData()
   {
     super.initData();
@@ -136,6 +145,7 @@ 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 ");
@@ -200,7 +210,7 @@ public class JPredFile extends AlignFile
             ascore = symbols.nextToken();
 
             Float score = new Float(ascore);
-            scores.addElement((Object) score);
+            scores.addElement(score);
           }
 
           Scores.put(id, scores);
@@ -211,16 +221,16 @@ public class JPredFile extends AlignFile
 
           for (int j = 0; j < i; j++)
           {
-            scores.setElementAt(
-                    (Object) ((Float) scores.elementAt(j)).toString(), j);
+            scores.setElementAt(((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);
@@ -260,7 +270,9 @@ public class JPredFile extends AlignFile
           }
 
           if (QuerySeqPosition == -1)
+          {
             QuerySeqPosition = ids.size();
+          }
           ids.addElement(name);
           noSeqs++;
         }
@@ -273,7 +285,7 @@ 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));
         }
       }
     }
@@ -289,16 +301,20 @@ public class JPredFile extends AlignFile
     {
       // Add all sequence like objects
       Sequence newSeq = new Sequence(ids.elementAt(i).toString(),
-              seq_entries.elementAt(i).toString(), 1, seq_entries
-                      .elementAt(i).toString().length());
+              seq_entries.elementAt(i).toString(), 1,
+              seq_entries.elementAt(i).toString().length());
 
       if (maxLength != seq_entries.elementAt(i).toString().length())
       {
-        throw new IOException(MessageManager.formatMessage("exception.jpredconcide_entry_has_unexpected_number_of_columns", new String[]{ids.elementAt(i).toString()}));
+        throw new IOException(MessageManager.formatMessage(
+                "exception.jpredconcide_entry_has_unexpected_number_of_columns",
+                new String[]
+                { ids.elementAt(i).toString() }));
       }
 
-      if ((newSeq.getName().startsWith("QUERY") || newSeq.getName()
-              .startsWith("align;")) && (QuerySeqPosition == -1))
+      if ((newSeq.getName().startsWith("QUERY")
+              || newSeq.getName().startsWith("align;"))
+              && (QuerySeqPosition == -1))
       {
         QuerySeqPosition = seqs.size();
       }
@@ -318,7 +334,10 @@ public class JPredFile extends AlignFile
       } catch (Exception e)
       {
         tal = null;
-        IOException ex = new IOException(MessageManager.formatMessage("exception.couldnt_parse_concise_annotation_for_prediction", new String[]{e.getMessage()}));
+        IOException ex = new IOException(MessageManager.formatMessage(
+                "exception.couldnt_parse_concise_annotation_for_prediction",
+                new String[]
+                { e.getMessage() }));
         e.printStackTrace(); // java 1.1 does not have :
                              // ex.setStackTrace(e.getStackTrace());
         throw ex;
@@ -337,28 +356,28 @@ public class JPredFile extends AlignFile
    * 
    * @return String
    */
-  public String print()
+  @Override
+  public String print(SequenceI[] sqs, boolean jvsuffix)
   {
     return "Not Supported";
   }
 
   /**
-   * DOCUMENT ME!
    * 
    * @param args
-   *          DOCUMENT ME!
+   * @j2sIgnore
    */
   public static void main(String[] args)
   {
     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)
@@ -389,7 +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);