From a853fae4d9d4dbc80e877741c017fca7ee80c59e Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 17 May 2006 16:52:58 +0000
Subject: [PATCH] added unofficial support for concise output parsing from the
 JNet server to extract the sequence profile.

---
 src/jalview/io/AppletFormatAdapter.java |    6 ++++-
 src/jalview/io/IdentifyFile.java        |    6 +++++
 src/jalview/io/JPredFile.java           |   37 ++++++++++++++++++++++++++-----
 3 files changed, 43 insertions(+), 6 deletions(-)

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 5f73898..5f228fb 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -100,7 +100,11 @@
                 {
                     afile = new PfamFile(inFile, type);
                 }
-
+                else if (format.equals("JnetFile"))
+                {
+                  afile = new JPredFile(inFile, type);
+                  ((JPredFile)afile).removeNonSequences();
+                }
 
                 return afile.getSeqsAsArray();
             }
diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index 2040769..6b32fe1 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -126,6 +126,12 @@ public class IdentifyFile
 
                     break;
                 }
+                else if (data.indexOf(":")<data.indexOf(",")) //  && data.indexOf(",")<data.indexOf(",", data.indexOf(",")))
+                {
+                  // file looks like a concise JNet file
+                  reply="JnetFile";
+                  break;
+                }
             }
 
             reader.close();
diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index f5ba7d6..0ee41b8 100755
--- a/src/jalview/io/JPredFile.java
+++ b/src/jalview/io/JPredFile.java
@@ -24,12 +24,11 @@
  */
 package jalview.io;
 
-import jalview.datamodel.*;
-
 import java.io.*;
-
 import java.util.*;
 
+import jalview.datamodel.*;
+
 
 /**
  * DOCUMENT ME!
@@ -264,12 +263,12 @@ public class JPredFile extends AlignFile
                 }
             }
         }
-
+        /* leave it to the parser user to actually check this.
         if (noSeqs < 1)
         {
             throw new IOException(
                 "JpredFile Parser: No sequence in the prediction!");
-        }
+        }*/
 
         maxLength = seq_entries.elementAt(0).toString().length();
 
@@ -339,6 +338,34 @@ public class JPredFile extends AlignFile
             e.printStackTrace();
         }
     }
+    Vector annotSeqs=null;
+  /**
+   * removeNonSequences
+   */
+  public void removeNonSequences()
+  {
+    if (annotSeqs!=null)
+      return;
+    annotSeqs = new Vector();
+    Vector newseqs = new Vector();
+    int i=0;
+    int j=seqs.size();
+    for (; i<QuerySeqPosition; i++)
+        annotSeqs.add(seqs.get(i));
+      // check that no stray annotations have been added at the end.
+      {
+        SequenceI sq = (SequenceI) seqs.get(j-1);
+        if (sq.getName().toUpperCase().startsWith("JPRED")) {
+          annotSeqs.add(sq);
+          seqs.remove(--j);
+        }
+      }
+    for (; i<j; i++)
+        newseqs.add(seqs.get(i));
+
+    seqs.clear();
+    seqs = newseqs;
+  }
 }
 
 
-- 
1.7.10.2