X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FSeqsetUtils.java;h=f5ca6512ecdeaecfd9506c86a90e8e0bd508b76a;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=cdcecc0b9fe40cf9d6c61432cce46ab41b4a8b2a;hpb=33c59ebddbc51bbd26bc4c8576ec17c1498b19e8;p=jalview.git

diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index cdcecc0..f5ca651 100755
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -1,7 +1,26 @@
+/*
+ * 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
+ */
 package jalview.analysis;
 
-import jalview.datamodel.SequenceI;
-import java.util.Hashtable;
+import java.util.*;
+
+import jalview.datamodel.*;
 
 /**
  * <p>Title: </p>
@@ -17,36 +36,230 @@ import java.util.Hashtable;
  */
 public class SeqsetUtils
 {
-  public static Hashtable uniquify(SequenceI[] sequences)
+
+  /**
+   * Store essential properties of a sequence in a hashtable for later recovery
+   *  Keys are Name, Start, End, SeqFeatures, PdbId
+   * @param seq SequenceI
+   * @return Hashtable
+   */
+  public static Hashtable SeqCharacterHash(SequenceI seq)
+  {
+    Hashtable sqinfo = new Hashtable();
+    sqinfo.put("Name", seq.getName());
+    sqinfo.put("Start", new Integer(seq.getStart()));
+    sqinfo.put("End", new Integer(seq.getEnd()));
+    if (seq.getDescription() != null)
+    {
+      sqinfo.put("Description", seq.getDescription());
+    }
+    Vector sfeat = new Vector();
+    jalview.datamodel.SequenceFeature[] sfarray = seq.getSequenceFeatures();
+    if (sfarray != null && sfarray.length > 0)
+    {
+      for (int i = 0; i < sfarray.length; i++)
+      {
+        sfeat.add(sfarray[i]);
+      }
+    }
+    sqinfo.put("SeqFeatures", sfeat);
+    sqinfo.put("PdbId",
+               (seq.getPDBId() != null) ? seq.getPDBId() : new Vector());
+    sqinfo.put("datasetSequence",
+               (seq.getDatasetSequence() != null) ? seq.getDatasetSequence() :
+               new Sequence("THISISAPLACEHOLDER", ""));
+    return sqinfo;
+  }
+
+  /**
+   * Recover essential properties of a sequence from a hashtable
+   * TODO: replace these methods with something more elegant.
+   * @param sq SequenceI
+   * @param sqinfo Hashtable
+   * @return boolean true if name was not updated from sqinfo Name entry
+   */
+  public static boolean SeqCharacterUnhash(SequenceI sq, Hashtable sqinfo)
+  {
+    boolean namePresent = true;
+    if (sqinfo == null)
+    {
+      return false;
+    }
+    String oldname = (String) sqinfo.get("Name");
+    Integer start = (Integer) sqinfo.get("Start");
+    Integer end = (Integer) sqinfo.get("End");
+    Vector sfeatures = (Vector) sqinfo.get(
+        "SeqFeatures");
+    Vector pdbid = (Vector) sqinfo.get("PdbId");
+    String description = (String) sqinfo.get("Description");
+    Sequence seqds = (Sequence) sqinfo.get("datasetSequence");
+    if (oldname == null)
+    {
+      namePresent = false;
+    }
+    else
+    {
+      sq.setName(oldname);
+    }
+    if (pdbid != null && pdbid.size() > 0)
+    {
+      sq.setPDBId(pdbid);
+    }
+
+    if ( (start != null) && (end != null))
+    {
+      sq.setStart(start.intValue());
+      sq.setEnd(end.intValue());
+    }
+
+    if ( (sfeatures != null) && (sfeatures.size() > 0))
+    {
+      SequenceFeature[] sfarray = (SequenceFeature[]) sfeatures.toArray();
+      sq.setSequenceFeatures(sfarray);
+    }
+    if (description != null)
+    {
+      sq.setDescription(description);
+    }
+    if ( (seqds != null) &&
+        ! (seqds.getName().equals("THISISAPLACEHOLDER") &&
+           seqds.getLength() == 0))
+    {
+      sq.setDatasetSequence(seqds);
+    }
+
+    return namePresent;
+  }
+
+  /**
+   * Form of the unique name used in uniquify for the i'th sequence in an ordered vector of sequences.
+   * @param i int
+   * @return String
+   */
+  public static String unique_name(int i)
+  {
+    return new String("Sequence" + i);
+  }
+
+  /**
+   * Generates a hash of SeqCharacterHash properties for each sequence
+   * in a sequence set, and optionally renames the sequences to an
+   * unambiguous 'safe' name.
+   * @param sequences SequenceI[]
+   * @param write_names boolean set this to rename each of the sequences to its unique_name(index) name
+   * @return Hashtable to be passed to @see deuniquify to recover original names (and properties) for renamed sequences
+   */
+  public static Hashtable uniquify(SequenceI[] sequences, boolean write_names)
   {
     // Generate a safely named sequence set and a hash to recover the sequence names
     Hashtable map = new Hashtable();
+    //String[] un_names = new String[sequences.length];
+
     for (int i = 0; i < sequences.length; i++)
     {
-      String safename = new String("Sequence" + i);
-      map.put(safename, sequences[i].getName());
-      sequences[i].setName(safename);
+      String safename = unique_name(i);
+      map.put(safename, SeqCharacterHash(sequences[i]));
+
+      if (write_names)
+      {
+        sequences[i].setName(safename);
+      }
     }
+
     return map;
   }
 
+  /**
+   * recover unsafe sequence names and original properties for a sequence
+   * set using a map generated by @see uniquify(sequences,true)
+   * @param map Hashtable
+   * @param sequences SequenceI[]
+   * @return boolean
+   */
   public static boolean deuniquify(Hashtable map, SequenceI[] sequences)
   {
-    // recover unsafe sequence names for a sequence set
-    boolean allfound = true;
-    for (int i = 0; i < sequences.length; i++)
+    jalview.analysis.SequenceIdMatcher matcher = new SequenceIdMatcher(
+        sequences);
+    SequenceI msq = null;
+    Enumeration keys = map.keys();
+    Vector unmatched = new Vector();
+    for (int i = 0, j = sequences.length; i < j; i++)
+    {
+      unmatched.add(sequences[i]);
+    }
+    while (keys.hasMoreElements())
     {
-      if (map.containsKey(sequences[i].getName()))
+      Object key = keys.nextElement();
+      if (key instanceof String)
       {
-        String unsafename = (String) map.get(sequences[i].getName());
-        sequences[i].setName(unsafename);
+        if ( (msq = matcher.findIdMatch( (String) key)) != null)
+        {
+          Hashtable sqinfo = (Hashtable) map.get(key);
+          unmatched.remove(msq);
+          SeqCharacterUnhash(msq, sqinfo);
+        }
+        else
+        {
+          System.err.println("Can't find '" + ( (String) key) +
+                             "' in uniquified alignment");
+        }
       }
-      else
+    }
+    if (unmatched.size() > 0)
+    {
+      System.err.println("Did not find matches for :");
+      for (Enumeration i = unmatched.elements(); i.hasMoreElements();
+           System.out.println( ( (SequenceI) i.nextElement()).getName()))
       {
-        allfound = false;
+        ;
       }
+      return false;
     }
-    return allfound;
+
+    return true;
   }
 
+  /**
+   * returns a subset of the sequenceI seuqences,
+   * including only those that contain at least one residue.
+   * @param sequences SequenceI[]
+   * @return SequenceI[]
+   */
+  public static SequenceI[] getNonEmptySequenceSet(SequenceI[] sequences)
+  {
+    // Identify first row of alignment with residues for prediction
+    boolean ungapped[] = new boolean[sequences.length];
+    int msflen = 0;
+    for (int i = 0, j = sequences.length; i < j; i++)
+    {
+      String tempseq = jalview.analysis.AlignSeq.extractGaps(
+          jalview.util.Comparison.GapChars,
+          sequences[i].getSequenceAsString());
+
+      if (tempseq.length() == 0)
+      {
+        ungapped[i] = false;
+      }
+      else
+      {
+        ungapped[i] = true;
+        msflen++;
+      }
+    }
+    if (msflen == 0)
+    {
+      return null; // no minimal set
+    }
+    // compose minimal set
+    SequenceI[] mset = new SequenceI[msflen];
+    for (int i = 0, j = sequences.length, k = 0; i < j; i++)
+    {
+      if (ungapped[i])
+      {
+        mset[k++] = sequences[i];
+      }
+    }
+    ungapped = null;
+    return mset;
+  }
 }