X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FJPredFile.java;h=0ee41b8c64a811653ecc74a395b3458ede94aedf;hb=a853fae4d9d4dbc80e877741c017fca7ee80c59e;hp=901c20493a6db43ae45f52646fedfc8d93571ae0;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index 901c204..0ee41b8 100755
--- a/src/jalview/io/JPredFile.java
+++ b/src/jalview/io/JPredFile.java
@@ -1,37 +1,34 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
 */
 
-/**
- * PredFile.java
- * JalviewX / Vamsas Project
- * JPred.seq.concise reader
+/**
+ * PredFile.java
+ * JalviewX / Vamsas Project
+ * JPred.seq.concise reader
  */
 package jalview.io;
 
-import jalview.datamodel.*;
-
-import jalview.util.*;
-
 import java.io.*;
-
 import java.util.*;
 
+import jalview.datamodel.*;
+
 
 /**
  * DOCUMENT ME!
@@ -121,8 +118,8 @@ public class JPredFile extends AlignFile
         conf = null;
     }
 
-    /**
- * parse a JPred concise file into a sequence-alignment like object.
+    /**
+ * parse a JPred concise file into a sequence-alignment like object.
  */
     public void parse() throws IOException
     {
@@ -245,7 +242,7 @@ public class JPredFile extends AlignFile
 
                     while (ids.lastIndexOf(name) > -1)
                     {
-                        name = id.substring(id.indexOf(";") + 1) + "_" + 1;
+                        name = id.substring(id.indexOf(";") + 1) + "_" + ++i;
                     }
 
                     ids.addElement(name);
@@ -266,12 +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();
 
@@ -285,9 +282,9 @@ public class JPredFile extends AlignFile
             if (!Symscores.containsKey(ids.elementAt(i)) &&
                     !isValidProteinSequence(newSeq.getSequence()))
             {
-                throw new IOException(
-                    "JPredConcise: Not a valid protein sequence - (" +
-                    ids.elementAt(i).toString() + ")");
+                throw new IOException("JPredConcise: "
+                                      +AppletFormatAdapter.INVALID_CHARACTERS +" : "
+                                      +ids.elementAt(i).toString() + ")");
             }
 
             if (maxLength != seq_entries.elementAt(i).toString().length())
@@ -307,10 +304,10 @@ public class JPredFile extends AlignFile
         }
     }
 
-    /**
- * print
- *
- * @return String
+    /**
+ * print
+ *
+ * @return String
    */
     public String print()
     {
@@ -341,50 +338,78 @@ 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;
+  }
 }
 
 
-/*
- StringBuffer out = new StringBuffer();
-
- out.append("START PRED\n");
- for (int i = 0; i < s[0].sequence.length(); i++)
- {
-  out.append(s[0].sequence.substring(i, i + 1) + " ");
-  out.append(s[1].sequence.substring(i, i + 1) + " ");
-  out.append(s[1].score[0].elementAt(i) + " ");
-  out.append(s[1].score[1].elementAt(i) + " ");
-  out.append(s[1].score[2].elementAt(i) + " ");
-  out.append(s[1].score[3].elementAt(i) + " ");
-
-  out.append("\n");
- }
- out.append("END PRED\n");
- return out.toString();
- }
-
-    public static void main(String[] args)
- {
-  try
-  {
-    BLCFile blc = new BLCFile(args[0], "File");
-    DrawableSequence[] s = new DrawableSequence[blc.seqs.size()];
-    for (int i = 0; i < blc.seqs.size(); i++)
-    {
-      s[i] = new DrawableSequence( (Sequence) blc.seqs.elementAt(i));
-    }
-    String out = BLCFile.print(s);
-
-    AlignFrame af = new AlignFrame(null, s);
-    af.resize(700, 500);
-    af.show();
-    System.out.println(out);
-  }
-  catch (java.io.IOException e)
-  {
-    System.out.println("Exception " + e);
-  }
- }
-
- }
+/*
+ StringBuffer out = new StringBuffer();
+
+ out.append("START PRED\n");
+ for (int i = 0; i < s[0].sequence.length(); i++)
+ {
+  out.append(s[0].sequence.substring(i, i + 1) + " ");
+  out.append(s[1].sequence.substring(i, i + 1) + " ");
+  out.append(s[1].score[0].elementAt(i) + " ");
+  out.append(s[1].score[1].elementAt(i) + " ");
+  out.append(s[1].score[2].elementAt(i) + " ");
+  out.append(s[1].score[3].elementAt(i) + " ");
+
+  out.append("\n");
+ }
+ out.append("END PRED\n");
+ return out.toString();
+ }
+
+    public static void main(String[] args)
+ {
+  try
+  {
+    BLCFile blc = new BLCFile(args[0], "File");
+    DrawableSequence[] s = new DrawableSequence[blc.seqs.size()];
+    for (int i = 0; i < blc.seqs.size(); i++)
+    {
+      s[i] = new DrawableSequence( (Sequence) blc.seqs.elementAt(i));
+    }
+    String out = BLCFile.print(s);
+
+    AlignFrame af = new AlignFrame(null, s);
+    af.resize(700, 500);
+    af.show();
+    System.out.println(out);
+  }
+  catch (java.io.IOException e)
+  {
+    System.out.println("Exception " + e);
+  }
+ }
+
+ }
  */