X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FSeqsetUtils.java;h=891e29523260abfa21b0091368fd532b61f658ce;hb=08f7a2be3977da8704dd4751de7245bcc6fc41c3;hp=0aa2bd5e359f63e1a4ae4dcf6982ca219bf478df;hpb=ccc0d91abe38690088a6050faba8ef66cde1f271;p=jalview.git

diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index 0aa2bd5..891e295 100755
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -1,85 +1,103 @@
 /*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview 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 3
  * 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.
- *
+ *  
+ * Jalview 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
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.analysis;
 
-import java.util.*;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
 
-import jalview.datamodel.*;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
 
-/**
- * <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
+   * 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()));
+    sqinfo.put("Start", Integer.valueOf(seq.getStart()));
+    sqinfo.put("End", Integer.valueOf(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)
+
+    Vector<SequenceFeature> sfeat = new Vector<SequenceFeature>();
+    List<SequenceFeature> sfs = seq.getFeatures().getAllFeatures();
+    sfeat.addAll(sfs);
+
+    if (seq.getDatasetSequence() == null)
     {
-      for (int i = 0; i < sfarray.length; i++)
-      {
-        sfeat.addElement(sfarray[i]);
-      }
+      sqinfo.put("SeqFeatures", sfeat);
+      sqinfo.put("PdbId",
+              (seq.getAllPDBEntries() != null) ? seq.getAllPDBEntries()
+                      : new Vector<PDBEntry>());
+    }
+    else
+    {
+      sqinfo.put("datasetSequence",
+              (seq.getDatasetSequence() != null) ? seq.getDatasetSequence()
+                      : new Sequence("THISISAPLACEHOLDER", ""));
     }
-    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
+   * 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)
   {
+    return SeqCharacterUnhash(sq, sqinfo, false, false);
+  }
+
+  /**
+   * restore some characteristics for a sequence from its hash
+   * @param sq
+   * @param sqinfo
+   * @param excludeLimits - when true, start/end is left unmodified
+   * @param excludeFeatures - when true, features are not restored from stashed vector
+   * @return true if sequence's name was modified
+   */
+          
+  public static boolean SeqCharacterUnhash(SequenceI sq, Hashtable sqinfo, boolean excludeLimits,boolean excludeFeatures)
+  {
     boolean namePresent = true;
     if (sqinfo == null)
     {
@@ -88,9 +106,9 @@ public class SeqsetUtils
     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");
+    Vector<SequenceFeature> sfeatures = (Vector<SequenceFeature>) sqinfo
+            .get("SeqFeatures");
+    Vector<PDBEntry> pdbid = (Vector<PDBEntry>) sqinfo.get("PdbId");
     String description = (String) sqinfo.get("Description");
     Sequence seqds = (Sequence) sqinfo.get("datasetSequence");
     if (oldname == null)
@@ -106,29 +124,28 @@ public class SeqsetUtils
       sq.setPDBId(pdbid);
     }
 
-    if ( (start != null) && (end != null))
+    if (!excludeLimits && (start != null) && (end != null))
     {
       sq.setStart(start.intValue());
       sq.setEnd(end.intValue());
     }
-
-    if ( (sfeatures != null) && (sfeatures.size() > 0))
+    // TODO: drop this completely since we should not manipulate sequenceFeatures as a vector any more
+    if (!excludeFeatures && sfeatures != null && !sfeatures.isEmpty())
     {
-      SequenceFeature[] sfarray = new SequenceFeature[sfeatures.size()];
-      for (int is=0,isize=sfeatures.size();is<isize;is++)
-      { 
-        sfarray[is] = (SequenceFeature) sfeatures.elementAt(is);
-      }
-      sq.setSequenceFeatures(sfarray);
+      sq.setSequenceFeatures(sfeatures);
     }
     if (description != null)
     {
       sq.setDescription(description);
     }
-    if ( (seqds != null) &&
-        ! (seqds.getName().equals("THISISAPLACEHOLDER") &&
-           seqds.getLength() == 0))
+    if ((seqds != null) && !(seqds.getName().equals("THISISAPLACEHOLDER")
+            && seqds.getLength() == 0))
     {
+      if (sfeatures != null)
+      {
+        System.err.println(
+                "Implementation error: setting dataset sequence for a sequence which has sequence features.\n\tDataset sequence features will not be visible.");
+      }
       sq.setDatasetSequence(seqds);
     }
 
@@ -136,8 +153,11 @@ public class SeqsetUtils
   }
 
   /**
-   * Form of the unique name used in uniquify for the i'th sequence in an ordered vector of sequences.
-   * @param i int
+   * 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)
@@ -146,18 +166,26 @@ public class SeqsetUtils
   }
 
   /**
-   * 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
+   * 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)
+  public static Hashtable uniquify(SequenceI[] sequences,
+          boolean write_names)
   {
-    // Generate a safely named sequence set and a hash to recover the sequence 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];
+    // String[] un_names = new String[sequences.length];
 
     for (int i = 0; i < sequences.length; i++)
     {
@@ -174,28 +202,40 @@ public class SeqsetUtils
   }
 
   /**
-   * 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[]
+   * 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)
   {
     return deuniquify(map, sequences, true);
   }
+
   /**
-   * 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[]
-   * @param quiet when false, don't complain about sequences without any data in the 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[]
+   * @param quiet
+   *          when false, don't complain about sequences without any data in the
+   *          map.
    * @return boolean
    */
-    public static boolean deuniquify(Hashtable map, SequenceI[] sequences, boolean quiet)
-    {
-          jalview.analysis.SequenceIdMatcher matcher = new SequenceIdMatcher(
-        sequences);
+  public static boolean deuniquify(Hashtable map, SequenceI[] sequences,
+          boolean quiet)
+  {
+    jalview.analysis.SequenceIdMatcher matcher = new SequenceIdMatcher(
+            sequences);
     SequenceI msq = null;
     Enumeration keys = map.keys();
     Vector unmatched = new Vector();
@@ -208,7 +248,7 @@ public class SeqsetUtils
       Object key = keys.nextElement();
       if (key instanceof String)
       {
-        if ( (msq = matcher.findIdMatch( (String) key)) != null)
+        if ((msq = matcher.findIdMatch((String) key)) != null)
         {
           Hashtable sqinfo = (Hashtable) map.get(key);
           unmatched.removeElement(msq);
@@ -217,18 +257,19 @@ public class SeqsetUtils
         else
         {
           if (!quiet)
-            {
-            System.err.println("Can't find '" + ( (String) key) +
-                             "' in uniquified alignment");
-            }
+          {
+            System.err.println("Can't find '" + ((String) key)
+                    + "' in uniquified alignment");
+          }
         }
       }
     }
     if (unmatched.size() > 0 && !quiet)
     {
       System.err.println("Did not find matches for :");
-      for (Enumeration i = unmatched.elements(); i.hasMoreElements();
-           System.out.println( ( (SequenceI) i.nextElement()).getName()))
+      for (Enumeration i = unmatched.elements(); i
+              .hasMoreElements(); System.out
+                      .println(((SequenceI) i.nextElement()).getName()))
       {
         ;
       }
@@ -239,9 +280,11 @@ public class SeqsetUtils
   }
 
   /**
-   * returns a subset of the sequenceI seuqences,
-   * including only those that contain at least one residue.
-   * @param sequences SequenceI[]
+   * 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)
@@ -252,8 +295,8 @@ public class SeqsetUtils
     for (int i = 0, j = sequences.length; i < j; i++)
     {
       String tempseq = jalview.analysis.AlignSeq.extractGaps(
-          jalview.util.Comparison.GapChars,
-          sequences[i].getSequenceAsString());
+              jalview.util.Comparison.GapChars,
+              sequences[i].getSequenceAsString());
 
       if (tempseq.length() == 0)
       {