From: jprocter <Jim Procter>
Date: Tue, 24 Oct 2006 08:11:22 +0000 (+0000)
Subject: fixes bug reported by Christopher Tan (help@jalview.org) - preservation of sequence... 
X-Git-Tag: Release_2_2~259
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=3d558ed2093c9d85699945ff70271f0be119b434

fixes bug reported by Christopher Tan (help@jalview.org) - preservation of sequence description in aligned sequences.
---

diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index 908d4e5..885305a 100755
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -1,222 +1,226 @@
-/*
- * 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
- */
-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;
-  }
-}
+/*
+ * 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
+ */
+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()));
+    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 = 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;
+  }
+}