X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FSeqsetUtils.java;h=2b21e5eb589bf1f2cb94563834923f26102bfdcf;hb=3d0101179759ef157b088ea135423cd909512d9f;hp=885305ace8fe46c8cce1139cf914a9663dcddb45;hpb=3d558ed2093c9d85699945ff70271f0be119b434;p=jalview.git

diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index 885305a..2b21e5e 100755
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -1,46 +1,43 @@
 /*
- * 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
+ * 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.*;
-
-/**
- * <p>Title: </p>
- *
- * <p>Description: </p>
- *
- * <p>Copyright: Copyright (c) 2004</p>
- *
- * <p>Company: Dundee University</p>
- *
- * @author not attributable
- * @version 1.0
- */
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Vector;
+
 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)
@@ -49,40 +46,58 @@ public class SeqsetUtils
     sqinfo.put("Name", seq.getName());
     sqinfo.put("Start", new Integer(seq.getStart()));
     sqinfo.put("End", new Integer(seq.getEnd()));
-    if (seq.getDescription()!=null)
+    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",""));
+    jalview.datamodel.SequenceFeature[] sfarray = seq.getSequenceFeatures();
+    if (sfarray != null && sfarray.length > 0)
+    {
+      for (int i = 0; i < sfarray.length; i++)
+      {
+        sfeat.addElement(sfarray[i]);
+      }
+    }
+    if (seq.getDatasetSequence() == null)
+    {
+      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", ""));
+    }
     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)
   {
     boolean namePresent = true;
-    if (sqinfo==null)
+    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");
+    Vector sfeatures = (Vector) 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)
     {
@@ -92,25 +107,38 @@ public class SeqsetUtils
     {
       sq.setName(oldname);
     }
-    if (pdbid!=null && pdbid.size()>0)
+    if (pdbid != null && pdbid.size() > 0)
     {
       sq.setPDBId(pdbid);
     }
 
-    if ( (start != null) && (end != null))
+    if ((start != null) && (end != null))
     {
       sq.setStart(start.intValue());
       sq.setEnd(end.intValue());
     }
 
-    if ((sfeatures != null) && (sfeatures.size()>0))
+    if ((sfeatures != null) && (sfeatures.size() > 0))
     {
-      SequenceFeature[] sfarray = (SequenceFeature[]) sfeatures.toArray();
+      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);
     }
-    if (description!=null)
+    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);
     }
 
@@ -118,8 +146,11 @@ 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)
@@ -128,18 +159,26 @@ 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++)
     {
@@ -152,75 +191,130 @@ public class SeqsetUtils
       }
     }
 
-
     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[]
+   * 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);
+    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.
+   * @return boolean
+   */
+  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();
-    for (int i=0, j=sequences.length; i<j; i++)
-      unmatched.add(sequences[i]);
-    while (keys.hasMoreElements()) {
+    for (int i = 0, j = sequences.length; i < j; i++)
+    {
+      unmatched.addElement(sequences[i]);
+    }
+    while (keys.hasMoreElements())
+    {
       Object key = keys.nextElement();
-      if (key instanceof String) {
-        if ((msq = matcher.findIdMatch((String) key))!=null) {
+      if (key instanceof String)
+      {
+        if ((msq = matcher.findIdMatch((String) key)) != null)
+        {
           Hashtable sqinfo = (Hashtable) map.get(key);
-          unmatched.remove(msq);
+          unmatched.removeElement(msq);
           SeqCharacterUnhash(msq, sqinfo);
         }
         else
         {
-          System.err.println("Can't find '"+((String) key)+"' in uniquified alignment");
+          if (!quiet)
+          {
+            System.err.println("Can't find '" + ((String) key)
+                    + "' in uniquified alignment");
+          }
         }
       }
     }
-    if (unmatched.size()>0) {
+    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()))
+      {
+        ;
+      }
       return false;
     }
 
     return true;
   }
+
   /**
-   * 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) {
-      // 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++;
-        }
+  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;
       }
-      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];
+      else
+      {
+        ungapped[i] = true;
+        msflen++;
       }
-      ungapped = null;
-      return mset;
+    }
+    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;
   }
 }