X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FSeqsetUtils.java;h=691b905fe282f389be490f5d7ddffbc0a4dec258;hb=173a7ca81c8d8c00f889fd4e3583cc8733d3d179;hp=cdcecc0b9fe40cf9d6c61432cce46ab41b4a8b2a;hpb=33c59ebddbc51bbd26bc4c8576ec17c1498b19e8;p=jalview.git

diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index cdcecc0..691b905 100755
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -1,52 +1,222 @@
-package jalview.analysis;
-
-import jalview.datamodel.SequenceI;
-import java.util.Hashtable;
-
-/**
- * <p>Title: </p>
- *
- * <p>Description: </p>
- *
- * <p>Copyright: Copyright (c) 2004</p>
- *
- * <p>Company: Dundee University</p>
- *
- * @author not attributable
- * @version 1.0
- */
-public class SeqsetUtils
-{
-  public static Hashtable uniquify(SequenceI[] sequences)
-  {
-    // Generate a safely named sequence set and a hash to recover the sequence names
-    Hashtable map = new Hashtable();
-    for (int i = 0; i < sequences.length; i++)
-    {
-      String safename = new String("Sequence" + i);
-      map.put(safename, sequences[i].getName());
-      sequences[i].setName(safename);
-    }
-    return map;
-  }
-
-  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++)
-    {
-      if (map.containsKey(sequences[i].getName()))
-      {
-        String unsafename = (String) map.get(sequences[i].getName());
-        sequences[i].setName(unsafename);
-      }
-      else
-      {
-        allfound = false;
-      }
-    }
-    return allfound;
-  }
-
-}
+/*
+ * 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
+ */
+package jalview.analysis;
+
+import java.util.*;
+
+import jalview.datamodel.*;
+
+/**
+ * <p>Title: </p>
+ *
+ * <p>Description: </p>
+ *
+ * <p>Copyright: Copyright (c) 2004</p>
+ *
+ * <p>Company: Dundee University</p>
+ *
+ * @author not attributable
+ * @version 1.0
+ */
+public class SeqsetUtils
+{
+
+  /**
+   * 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()));
+    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");
+    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 ((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 = 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)
+  {
+    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()) {
+      Object key = keys.nextElement();
+      if (key instanceof String) {
+        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");
+        }
+      }
+    }
+    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()))
+           ;
+      return false;
+    }
+
+    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].getSequence());
+        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;
+  }
+}