X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJPredFile.java;h=dfe1ecf920550e02e1c2dc65e89133f6b2195fe8;hb=f683f4d6c8af43be0ffeb96513b52572619efed5;hp=754b539eead65bcb98709fd2470a42850e67fb2c;hpb=950f8f47f9eff65f5f39501789b03f03591f1819;p=jalview.git

diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index 754b539..dfe1ecf 100755
--- a/src/jalview/io/JPredFile.java
+++ b/src/jalview/io/JPredFile.java
@@ -1,3 +1,22 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 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
@@ -5,12 +24,23 @@
  */
 package jalview.io;
 
-import jalview.datamodel.*;
-import jalview.util.*;
-
 import java.io.*;
 import java.util.*;
 
+import jalview.datamodel.*;
+
+/**
+ * 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 prediction annotation (anything else). 
+ * Automagic translation happens for annotation called 'JNETPRED' (translated to Secondary Structure Prediction), or 'JNETCONF' (translates to 'Prediction Confidence').
+ * Numeric scores are differentiated from symbolic by being parseable into a float vector. They are put in Scores.
+ * Symscores gets the others.
+ * JNetAnnotationMaker translates the data parsed by this object into annotation on an alignment. It is automatically called
+ * but can be used to transfer the annotation onto a sequence in another alignment (and insert gaps where necessary)
+ * @author jprocter
+ * @version $Revision$
+ */
 public class JPredFile
     extends AlignFile
 {
@@ -18,57 +48,112 @@ public class JPredFile
   Vector conf;
   Hashtable Scores; // Hash of names and score vectors
   Hashtable Symscores; // indexes of symbol annotation properties in sequenceI vector
-  public JPredFile(String inStr)
+  private int QuerySeqPosition;
+
+  /**
+   * Creates a new JPredFile object.
+   *
+   * @param inFile DOCUMENT ME!
+   * @param type DOCUMENT ME!
+   *
+   * @throws IOException DOCUMENT ME!
+   */
+  public JPredFile(String inFile, String type)
+      throws IOException
+  {
+    super(inFile, type);
+  }
+  public JPredFile(FileParse source) throws IOException
+  {
+    super(source);
+  }
+  /**
+   * DOCUMENT ME!
+   *
+   * @param QuerySeqPosition DOCUMENT ME!
+   */
+  public void setQuerySeqPosition(int QuerySeqPosition)
   {
-    super(inStr);
+    this.QuerySeqPosition = QuerySeqPosition;
   }
 
-  public void initData()
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int getQuerySeqPosition()
   {
+    return QuerySeqPosition;
+  }
 
-    super.initData();
-    Scores = new Hashtable();
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Hashtable getScores()
+  {
+    return Scores;
   }
 
-  public JPredFile(String inFile, String type)
-      throws IOException
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Hashtable getSymscores()
   {
+    return Symscores;
+  }
 
-    super(inFile, type);
+  /**
+   * DOCUMENT ME!
+   */
+  public void initData()
+  {
+    super.initData();
+    Scores = new Hashtable();
+    ids = null;
+    conf = null;
   }
 
   /**
    * parse a JPred concise file into a sequence-alignment like object.
    */
-
   public void parse()
       throws IOException
   {
-
+    // JBPNote log.System.out.println("all read in ");
     String line;
-
+    QuerySeqPosition = -1;
     noSeqs = 0;
+
     Vector seq_entries = new Vector();
     Vector ids = new Vector();
     Hashtable Symscores = new Hashtable();
+
     while ( (line = nextLine()) != null)
     {
       // Concise format allows no comments or non comma-formatted data
       StringTokenizer str = new StringTokenizer(line, ":");
       String id = "";
-      String seq = "";
+
       if (!str.hasMoreTokens())
       {
         continue;
       }
 
       id = str.nextToken();
+
       String seqsym = str.nextToken();
       StringTokenizer symbols = new StringTokenizer(seqsym, ",");
+
       // decide if we have more than just alphanumeric symbols
       int numSymbols = symbols.countTokens();
 
-      if (numSymbols==0) {
+      if (numSymbols == 0)
+      {
         continue;
       }
 
@@ -78,193 +163,274 @@ public class JPredFile
         if (Scores.containsKey(id))
         {
           int i = 1;
+
           while (Scores.containsKey(id + "_" + i))
           {
             i++;
           }
+
           id = id + "_" + i;
         }
+
         Vector scores = new Vector();
+
         // Typecheck from first entry
         int i = 0;
-        String ascore="dead";
+        String ascore = "dead";
+
         try
         {
           // store elements as floats...
-          while (symbols.hasMoreTokens()) {
+          while (symbols.hasMoreTokens())
+          {
             ascore = symbols.nextToken();
+
             Float score = new Float(ascore);
             scores.addElement( (Object) score);
           }
+
           Scores.put(id, scores);
         }
         catch (Exception e)
         {
           // or just keep them as strings
           i = scores.size();
+
           for (int j = 0; j < i; j++)
           {
-            scores.set(j,
-                       (Object) ( (Float) scores.get(j)).toString());
+            scores.setElementAt(
+                (Object) ( (Float) scores.elementAt(j)).toString(), j);
           }
-          scores.addElement((Object) ascore);
-          while (symbols.hasMoreTokens()) {
-            {
-              ascore = symbols.nextToken();
-              scores.addElement( (Object) ascore);
-            }
+
+          scores.addElement( (Object) ascore);
+
+          while (symbols.hasMoreTokens())
+          {
+            ascore = symbols.nextToken();
+            scores.addElement( (Object) ascore);
           }
+
           Scores.put(id, scores);
         }
-      } else
-      if (id.equals("jnetconf"))
+      }
+      else if (id.equals("jnetconf"))
       {
+        // log.debug System.out.println("here");
         id = "Prediction Confidence";
         this.conf = new Vector(numSymbols);
+
         for (int i = 0; i < numSymbols; i++)
         {
-          conf.set(i, (Object) symbols.nextToken());
+          conf.setElementAt(symbols.nextToken(), i);
         }
       }
       else
+      {
+        // Sequence or a prediction string (rendered as sequence)
+        StringBuffer newseq = new StringBuffer();
+
+        for (int i = 0; i < numSymbols; i++)
         {
-          // Sequence or a prediction string (rendered as sequence)
+          newseq.append(symbols.nextToken());
+        }
 
-          StringBuffer newseq = new StringBuffer();
+        if (id.indexOf(";") > -1)
+        {
+          seq_entries.addElement(newseq);
 
-          for (int i = 0; i < numSymbols; i++) {
-            newseq.append(symbols.nextToken());
-          }
+          int i = 1;
+          String name = id.substring(id.indexOf(";") + 1);
 
-          if (id.indexOf(";") > -1) {
-            seq_entries.addElement(newseq);
-            int i=1;
-            String name = id.substring(id.indexOf(";")+1);
-            while (ids.lastIndexOf(name)>-1) {
-              name = id.substring(id.indexOf(";")+1)+"_"+1;
-            }
-            ids.addElement(name);
-            noSeqs++;
+          while (ids.lastIndexOf(name) > -1)
+          {
+            name = id.substring(id.indexOf(";") + 1) + "_" + ++i;
           }
-          else
+
+          if (QuerySeqPosition==-1)
+            QuerySeqPosition = ids.size();
+          ids.addElement(name);
+          noSeqs++;
+        }
+        else
+        {
+          if (id.equals("JNETPRED"))
           {
-            if (id.equals("JNETPRED")) {
-              id = "Predicted Secondary Structure";
-            }
-            seq_entries.addElement( newseq.toString() );
-            ids.addElement(id);
-            Symscores.put((Object) id, (Object) new Integer(ids.size()-1));
+            id = "Predicted Secondary Structure";
           }
+
+          seq_entries.addElement(newseq.toString());
+          ids.addElement(id);
+          Symscores.put( (Object) id,
+                        (Object)new Integer(ids.size() - 1));
+        }
       }
     }
+    /* leave it to the parser user to actually check this.
+             if (noSeqs < 1)
+             {
+        throw new IOException(
+            "JpredFile Parser: No sequence in the prediction!");
+             }*/
 
-
-    if (noSeqs < 1)
-    {
-      throw new IOException(
-      "JpredFile Parser: No sequence in the prediction!");
-    }
     maxLength = seq_entries.elementAt(0).toString().length();
+
     for (int i = 0; i < ids.size(); i++)
     {
       // 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());
-      if (!Symscores.containsKey(ids.elementAt(i))
-          && !isValidProteinSequence(newSeq.getSequence()))
-      {
-        throw new IOException(
-      "JPredConcise: Not a valid protein sequence - ("
-      + ids.elementAt(i).toString() + ")");
-      }
+                                     seq_entries.elementAt(i).toString().length());
 
       if (maxLength != seq_entries.elementAt(i).toString().length())
       {
         throw new IOException("JPredConcise: Entry (" +
-                              ids.elementAt(i).toString()
-                              + ") has an unexpected number of columns");
+                              ids.elementAt(i).toString() +
+                              ") has an unexpected number of columns");
       }
-      seqs.addElement(newSeq);
 
+      if ((newSeq.getName().startsWith("QUERY") || newSeq.getName().startsWith("align;"))&&
+          (QuerySeqPosition == -1))
+      {
+        QuerySeqPosition = seqs.size();
+      }
+
+      seqs.addElement(newSeq);
     }
+    if (seqs.size()>0)
+    {
+      // try to make annotation for a prediction only input (default if no alignment is given)
+      Alignment tal = new Alignment(this.getSeqsAsArray());
+      try {
+        JnetAnnotationMaker.add_annotation(this, tal, QuerySeqPosition, true);
+      } catch (Exception e)
+      {
+        tal = null;
+        IOException ex = new IOException("Couldn't parse concise annotation for prediction profile.\n"+e);
+        throw ex;
+      }
+      this.annotations = new Vector();
+      AlignmentAnnotation[] aan = tal.getAlignmentAnnotation();
+      for (int aai = 0; aan!=null && aai<aan.length; aai++)
+      {
+        annotations.addElement(aan[aai]);
+      }
+    } 
   }
 
   /**
    * print
    *
    * @return String
-     */
+   */
+  public String print()
+  {
+    return "Not Supported";
+  }
 
-    public String print()
+  /**
+   * DOCUMENT ME!
+   *
+   * @param args DOCUMENT ME!
+   */
+  public static void main(String[] args)
+  {
+    try
     {
-      return "Not Supported";
-    }
+      JPredFile blc = new JPredFile(args[0], "File");
 
-    public static void main(String[] args)
-    {
-      try
-      {
-        JPredFile blc = new JPredFile(args[0], "File");
-        for (int i = 0; i < blc.seqs.size(); i++)
-        {
-          System.out.println( ( (Sequence) blc.seqs.elementAt(i)).getName()
-                             + "\n" +
-                             ( (Sequence) blc.seqs.elementAt(i)).getSequence()
-                             + "\n");
-        }
-      }
-      catch (java.io.IOException e)
+      for (int i = 0; i < blc.seqs.size(); i++)
       {
-        System.out.println("Exception " + e);
-        e.printStackTrace();
+        System.out.println( ( (Sequence) blc.seqs.elementAt(i)).getName() +
+                           "\n" +
+                           ( (Sequence) blc.seqs.elementAt(i)).getSequenceAsString() +
+                           "\n");
       }
     }
+    catch (java.io.IOException e)
+    {
+      System.err.println("Exception " + e);
+      // e.printStackTrace(); not java 1.1 compatible!
+    }
   }
 
-  /*
-   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
+  Vector annotSeqs = null;
+  /**
+   * removeNonSequences
+   */
+  public void removeNonSequences()
+  {
+    if (annotSeqs != null)
     {
-      BLCFile blc = new BLCFile(args[0], "File");
-      DrawableSequence[] s = new DrawableSequence[blc.seqs.size()];
-      for (int i = 0; i < blc.seqs.size(); i++)
+      return;
+    }
+    annotSeqs = new Vector();
+    Vector newseqs = new Vector();
+    int i = 0;
+    int j = seqs.size();
+    for (; i < QuerySeqPosition; i++)
+    {
+      annotSeqs.addElement(seqs.elementAt(i));
+    }
+    // check that no stray annotations have been added at the end.
+    {
+      SequenceI sq = (SequenceI) seqs.elementAt(j - 1);
+      if (sq.getName().toUpperCase().startsWith("JPRED"))
       {
-        s[i] = new DrawableSequence( (Sequence) blc.seqs.elementAt(i));
+        annotSeqs.addElement(sq);
+        seqs.removeElementAt(--j);
       }
-      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)
+    for (; i < j; i++)
     {
-      System.out.println("Exception " + e);
+      newseqs.addElement(seqs.elementAt(i));
     }
-   }
 
-   }
-   */
+    seqs.removeAllElements();
+    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);
+  }
+ }
+
+ }
+ */