X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FSeqsetUtils.java;h=21dea5793b0b56306c1fcf51c0ba995d6b2b3669;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=a86775d5c4e44f46eb7fd23ad002ff395cc71fbb;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git

diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index a86775d..21dea57 100755
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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 file is part of Jalview.
  * 
- * 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 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.
  * 
- * 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
+ * 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.analysis;
 
@@ -22,26 +21,6 @@ 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
 {
 
@@ -50,7 +29,7 @@ public class SeqsetUtils
    * Keys are Name, Start, End, SeqFeatures, PdbId
    * 
    * @param seq
-   *                SequenceI
+   *          SequenceI
    * @return Hashtable
    */
   public static Hashtable SeqCharacterHash(SequenceI seq)
@@ -75,8 +54,9 @@ public class SeqsetUtils
     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", ""));
+    sqinfo.put("datasetSequence",
+            (seq.getDatasetSequence() != null) ? seq.getDatasetSequence()
+                    : new Sequence("THISISAPLACEHOLDER", ""));
     return sqinfo;
   }
 
@@ -85,9 +65,9 @@ public class SeqsetUtils
    * these methods with something more elegant.
    * 
    * @param sq
-   *                SequenceI
+   *          SequenceI
    * @param sqinfo
-   *                Hashtable
+   *          Hashtable
    * @return boolean true if name was not updated from sqinfo Name entry
    */
   public static boolean SeqCharacterUnhash(SequenceI sq, Hashtable sqinfo)
@@ -151,7 +131,7 @@ public class SeqsetUtils
    * ordered vector of sequences.
    * 
    * @param i
-   *                int
+   *          int
    * @return String
    */
   public static String unique_name(int i)
@@ -165,10 +145,10 @@ public class SeqsetUtils
    * name.
    * 
    * @param sequences
-   *                SequenceI[]
+   *          SequenceI[]
    * @param write_names
-   *                boolean set this to rename each of the sequences to its
-   *                unique_name(index) name
+   *          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
@@ -201,9 +181,9 @@ public class SeqsetUtils
    * 
    * @see uniquify(sequences,true)
    * @param map
-   *                Hashtable
+   *          Hashtable
    * @param sequences
-   *                SequenceI[]
+   *          SequenceI[]
    * @return boolean
    */
   public static boolean deuniquify(Hashtable map, SequenceI[] sequences)
@@ -217,12 +197,12 @@ public class SeqsetUtils
    * 
    * @see uniquify(sequences,true)
    * @param map
-   *                Hashtable
+   *          Hashtable
    * @param sequences
-   *                SequenceI[]
+   *          SequenceI[]
    * @param quiet
-   *                when false, don't complain about sequences without any data
-   *                in the map.
+   *          when false, don't complain about sequences without any data in the
+   *          map.
    * @return boolean
    */
   public static boolean deuniquify(Hashtable map, SequenceI[] sequences,
@@ -277,7 +257,7 @@ public class SeqsetUtils
    * contain at least one residue.
    * 
    * @param sequences
-   *                SequenceI[]
+   *          SequenceI[]
    * @return SequenceI[]
    */
   public static SequenceI[] getNonEmptySequenceSet(SequenceI[] sequences)
@@ -288,8 +268,8 @@ 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)
       {