X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJPredFile.java;h=c431cc4ef51686f25614952749df7cf691a5f7a0;hb=6af1258218f8fdbb2d9d6794e72db4c41ec8bf48;hp=0ee41b8c64a811653ecc74a395b3458ede94aedf;hpb=a853fae4d9d4dbc80e877741c017fca7ee80c59e;p=jalview.git

diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index 0ee41b8..c431cc4 100755
--- a/src/jalview/io/JPredFile.java
+++ b/src/jalview/io/JPredFile.java
@@ -1,415 +1,406 @@
-/*
-* 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
- */
-package jalview.io;
-
-import java.io.*;
-import java.util.*;
-
-import jalview.datamodel.*;
-
-
-/**
- * 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 inStr DOCUMENT ME!
-     */
-    public JPredFile(String inStr)
-    {
-        super(inStr);
-    }
-
-    /**
-     * 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);
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param QuerySeqPosition DOCUMENT ME!
-     */
-    public void setQuerySeqPosition(int QuerySeqPosition)
-    {
-        this.QuerySeqPosition = QuerySeqPosition;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getQuerySeqPosition()
-    {
-        return QuerySeqPosition;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Hashtable getScores()
-    {
-        return Scores;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Hashtable getSymscores()
-    {
-        return Symscores;
-    }
-
-    /**
-     * 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 = "";
-
-            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)
-            {
-                continue;
-            }
-
-            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.set(j,
-                            (Object) ((Float) scores.get(j)).toString());
-                    }
-
-                    scores.addElement((Object) ascore);
-
-                    while (symbols.hasMoreTokens())
-                    {
-                        ascore = symbols.nextToken();
-                        scores.addElement((Object) ascore);
-                    }
-
-                    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();
-
-                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();
-
-        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: "
-                                      +AppletFormatAdapter.INVALID_CHARACTERS +" : "
-                                      +ids.elementAt(i).toString() + ")");
-            }
-
-            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();
-            }
-
-            seqs.addElement(newSeq);
-        }
-    }
-
-    /**
- * print
- *
- * @return String
-   */
-    public String print()
-    {
-        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++)
-            {
-                System.out.println(((Sequence) blc.seqs.elementAt(i)).getName() +
-                    "\n" + ((Sequence) blc.seqs.elementAt(i)).getSequence() +
-                    "\n");
-            }
-        }
-        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.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);
-  }
- }
-
- }
- */
+/*
+* 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
+ * JPred.seq.concise reader
+ */
+package jalview.io;
+
+import java.io.*;
+import java.util.*;
+
+import jalview.datamodel.*;
+
+
+/**
+ * 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);
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param QuerySeqPosition DOCUMENT ME!
+     */
+    public void setQuerySeqPosition(int QuerySeqPosition)
+    {
+        this.QuerySeqPosition = QuerySeqPosition;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getQuerySeqPosition()
+    {
+        return QuerySeqPosition;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Hashtable getScores()
+    {
+        return Scores;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Hashtable getSymscores()
+    {
+        return Symscores;
+    }
+
+    /**
+     * 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 = "";
+
+            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)
+            {
+                continue;
+            }
+
+            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);
+                }
+            }
+            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);
+                }
+            }
+            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();
+
+        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: "
+                                      +AppletFormatAdapter.INVALID_CHARACTERS +" : "
+                                      +ids.elementAt(i).toString() + ")");
+            }
+
+            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();
+            }
+
+            seqs.addElement(newSeq);
+        }
+    }
+
+    /**
+ * print
+ *
+ * @return String
+   */
+    public String print()
+    {
+        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++)
+            {
+                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();
+        }
+    }
+    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.
+      {
+        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)
+  {
+    System.out.println("Exception " + e);
+  }
+ }
+
+ }
+ */