X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJPredFile.java;h=c431cc4ef51686f25614952749df7cf691a5f7a0;hb=312a01c56639fe2d5a94a7918e6968955533afc5;hp=b2226db7ec67cc0b6e8711f1cc98b32d0d29a0ca;hpb=e5127e5f27f02c8f328539eaac68eabfbee1d135;p=jalview.git

diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index b2226db..c431cc4 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) 2006 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
@@ -5,289 +24,383 @@
  */
 package jalview.io;
 
-import jalview.datamodel.*;
-import jalview.util.*;
-
 import java.io.*;
 import java.util.*;
 
-public class JPredFile
-    extends AlignFile
-{
-  Vector ids;
-  Vector conf;
-  Hashtable Scores; // Hash of names and score vectors
-  Hashtable Symscores; // indexes of symbol annotation properties in sequenceI vector
-  private int QuerySeqPosition;
-  public void setQuerySeqPosition(int QuerySeqPosition)
-  {
-    this.QuerySeqPosition = QuerySeqPosition;
-  }
+import jalview.datamodel.*;
 
-  public int getQuerySeqPosition()
-  {
-    return QuerySeqPosition;
-  }
-  public Hashtable getScores() {
-    return Scores;
-  }
-  public Hashtable getSymscores() {
-    return Symscores;
-  }
 
-  public JPredFile(String inStr)
-  {
-    super(inStr);
-  }
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class JPredFile extends AlignFile
+{
+    Vector ids;
+    Vector conf;
+    Hashtable Scores; // Hash of names and score vectors
+    Hashtable Symscores; // indexes of symbol annotation properties in sequenceI vector
+    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 void initData()
-  {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param QuerySeqPosition DOCUMENT ME!
+     */
+    public void setQuerySeqPosition(int QuerySeqPosition)
+    {
+        this.QuerySeqPosition = QuerySeqPosition;
+    }
 
-    super.initData();
-    Scores = new Hashtable();
-    ids = null;
-    conf = null;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getQuerySeqPosition()
+    {
+        return QuerySeqPosition;
+    }
 
-  public JPredFile(String inFile, String type)
-      throws IOException
-  {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Hashtable getScores()
+    {
+        return Scores;
+    }
 
-    super(inFile, type);
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Hashtable getSymscores()
+    {
+        return Symscores;
+    }
 
-  /**
-   * 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)
+    /**
+     * DOCUMENT ME!
+     */
+    public void initData()
     {
-      // Concise format allows no comments or non comma-formatted data
-      StringTokenizer str = new StringTokenizer(line, ":");
-      String id = "";
-      if (!str.hasMoreTokens())
-      {
-        continue;
-      }
+        super.initData();
+        Scores = new Hashtable();
+        ids = null;
+        conf = null;
+    }
 
-      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();
+    /**
+ * 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;
 
-      if (numSymbols==0) {
-        continue;
-      }
+        Vector seq_entries = new Vector();
+        Vector ids = new Vector();
+        Hashtable Symscores = new Hashtable();
 
-      if (seqsym.length() != (2 * numSymbols))
-      {
-        // Set of scalars for some property
-        if (Scores.containsKey(id))
+        while ((line = nextLine()) != null)
         {
-          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";
-        try
-        {
-          // store elements as floats...
-          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.addElement((Object) ascore);
-          while (symbols.hasMoreTokens()) {
+            // Concise format allows no comments or non comma-formatted data
+            StringTokenizer str = new StringTokenizer(line, ":");
+            String id = "";
+
+            if (!str.hasMoreTokens())
             {
-              ascore = symbols.nextToken();
-              scores.addElement( (Object) ascore);
+                continue;
             }
-          }
-          Scores.put(id, scores);
-        }
-      }
-      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());
-        }
-      }
-      else
-        {
-          // Sequence or a prediction string (rendered as sequence)
 
-          StringBuffer newseq = new StringBuffer();
+            id = str.nextToken();
 
-          for (int i = 0; i < numSymbols; i++) {
-            newseq.append(symbols.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)
+            {
+                continue;
+            }
 
-          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;
+            if (seqsym.length() != (2 * numSymbols))
+            {
+                // Set of scalars for some property
+                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";
+
+                try
+                {
+                    // store elements as floats...
+                    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.setElementAt(
+                            (Object) ((Float) scores.elementAt(j)).toString(), j);
+                    }
+
+                    scores.addElement((Object) ascore);
+
+                    while (symbols.hasMoreTokens())
+                    {
+                        ascore = symbols.nextToken();
+                        scores.addElement((Object) ascore);
+                    }
+
+                    Scores.put(id, scores);
+                }
             }
-            ids.addElement(name);
-
-            noSeqs++;
-          }
-          else
-          {
-            if (id.equals("JNETPRED")) {
-              id = "Predicted Secondary Structure";
+            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.setElementAt( symbols.nextToken(), i);
+                }
             }
-            seq_entries.addElement( newseq.toString() );
-            ids.addElement(id);
-            Symscores.put((Object) id, (Object) new Integer(ids.size()-1));
-          }
-      }
-    }
+            else
+            {
+                // Sequence or a prediction string (rendered as sequence)
+                StringBuffer newseq = new StringBuffer();
+
+                for (int i = 0; i < numSymbols; i++)
+                {
+                    newseq.append(symbols.nextToken());
+                }
+
+                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) + "_" + ++i;
+                    }
+
+                    ids.addElement(name);
+
+                    noSeqs++;
+                }
+                else
+                {
+                    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));
+                }
+            }
+        }
+        /* 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();
 
-    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() + ")");
-      }
+        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 (maxLength != seq_entries.elementAt(i).toString().length())
-      {
-        throw new IOException("JPredConcise: Entry (" +
-                              ids.elementAt(i).toString()
-                              + ") has an unexpected number of columns");
-      }
-      if (newSeq.getName().startsWith("QUERY") && QuerySeqPosition==-1) {
-        QuerySeqPosition = seqs.size();
-      }
+            if (!Symscores.containsKey(ids.elementAt(i)) &&
+                    !isValidProteinSequence(newSeq.getSequence()))
+            {
+                throw new IOException("JPredConcise: "
+                                      +AppletFormatAdapter.INVALID_CHARACTERS +" : "
+                                      +ids.elementAt(i).toString() + ")");
+            }
 
-      seqs.addElement(newSeq);
+            if (maxLength != seq_entries.elementAt(i).toString().length())
+            {
+                throw new IOException("JPredConcise: Entry (" +
+                    ids.elementAt(i).toString() +
+                    ") has an unexpected number of columns");
+            }
 
-    }
-  }
+            if (newSeq.getName().startsWith("QUERY") &&
+                    (QuerySeqPosition == -1))
+            {
+                QuerySeqPosition = seqs.size();
+            }
 
-  /**
-   * print
-   *
-   * @return String
-     */
+            seqs.addElement(newSeq);
+        }
+    }
 
+    /**
+ * print
+ *
+ * @return String
+   */
     public String print()
     {
-      return "Not Supported";
+        return "Not Supported";
     }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param args DOCUMENT ME!
+     */
     public static void main(String[] args)
     {
-      try
-      {
-        JPredFile blc = new JPredFile(args[0], "File");
-        for (int i = 0; i < blc.seqs.size(); i++)
+        try
         {
-          System.out.println( ( (Sequence) blc.seqs.elementAt(i)).getName()
-                             + "\n" +
-                             ( (Sequence) blc.seqs.elementAt(i)).getSequence()
-                             + "\n");
+            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)).getSequenceAsString() +
+                    "\n");
+            }
         }
-      }
-      catch (java.io.IOException e)
+        catch (java.io.IOException e)
+        {
+            System.err.println("Exception " + e);
+            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.addElement(seqs.elementAt(i));
+      // check that no stray annotations have been added at the end.
       {
-        System.err.println("Exception " + e);
-        e.printStackTrace();
+        SequenceI sq = (SequenceI) seqs.elementAt(j-1);
+        if (sq.getName().toUpperCase().startsWith("JPRED")) {
+          annotSeqs.addElement(sq);
+          seqs.removeElementAt(--j);
+        }
       }
-    }
+    for (; i<j; i++)
+        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)
+/*
+ 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++)
     {
-      System.out.println("Exception " + e);
+      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);
+  }
+ }
+
+ }
+ */