X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FSeqsetUtils.java;h=8a8ae282d8a9dcef1c4130138117ed4fdbfd677c;hb=588042b69abf8e60bcc950b24c283933c7dd422f;hp=faa08e1e65cc8232488dad3532e3df8682097a0e;hpb=5cd8e373c75fb348ecda4d94d8a46468fb92756d;p=jalview.git

diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index faa08e1..8a8ae28 100755
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -15,13 +15,14 @@
 * 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 jalview.datamodel.SequenceI;
-import java.util.Hashtable;
-
+*/
+package jalview.analysis;
+
+import jalview.datamodel.SequenceI;
+
+import java.util.Hashtable;
+
+
 /**
  * <p>Title: </p>
  *
@@ -33,97 +34,105 @@ import java.util.Hashtable;
  *
  * @author not attributable
  * @version 1.0
- */
-public class SeqsetUtils
-{
+ */
+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()));
-    sqinfo.put("SeqFeatures", seq.getSequenceFeatures());
-    sqinfo.put("PdbId", (seq.getPDBId()!=null) ? seq.getPDBId() : new String("") );
-    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
-   */
-  public static boolean SeqCharacterUnhash(SequenceI sq, Hashtable sqinfo) {
-    boolean namePresent = true;
-    String oldname = (String) sqinfo.get("Name");
-    Integer start = (Integer) sqinfo.get("Start");
-    Integer end = (Integer) sqinfo.get("End");
-    java.util.Vector sfeatures = (java.util.Vector) sqinfo.get("SeqFeatures");
-    String pdbid = (String) sqinfo.get("PdbId");
-    if (oldname==null)
-      namePresent = false;
-    else
-      sq.setName(oldname);
-    if (!pdbid.equals(""))
-      sq.setPDBId(pdbid);
-
-    if ((start!=null) && (end!=null)) {
-      sq.setStart(start.intValue());
-      sq.setEnd(end.intValue());
-    }
-    if (sfeatures!=null)
-      sq.setSequenceFeatures(sfeatures);
-    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);
-  }
-
-  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];
-    if (!write_names)
-
-    for (int i = 0; i < sequences.length; i++)
-    {
-      String safename = new String("Sequence" + i);
-      map.put(safename, SeqCharacterHash(sequences[i]));
-      if (write_names)
-        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()))
-      {
-        Hashtable sqinfo = (Hashtable) map.get(sequences[i].getName());
-        SeqCharacterUnhash(sequences[i], sqinfo);
-      }
-      else
-      {
-        allfound = false;
-      }
-    }
-    return allfound;
-  }
-
-}
+ * 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()));
+        sqinfo.put("SeqFeatures", seq.getSequenceFeatures());
+        sqinfo.put("PdbId",
+            (seq.getPDBId() != null) ? seq.getPDBId() : new String(""));
+
+        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
+ */
+    public static boolean SeqCharacterUnhash(SequenceI sq, Hashtable sqinfo) {
+        boolean namePresent = true;
+        String oldname = (String) sqinfo.get("Name");
+        Integer start = (Integer) sqinfo.get("Start");
+        Integer end = (Integer) sqinfo.get("End");
+        java.util.Vector sfeatures = (java.util.Vector) sqinfo.get(
+                "SeqFeatures");
+        String pdbid = (String) sqinfo.get("PdbId");
+
+        if (oldname == null) {
+            namePresent = false;
+        } else {
+            sq.setName(oldname);
+        }
+
+        if (!pdbid.equals("")) {
+            sq.setPDBId(pdbid);
+        }
+
+        if ((start != null) && (end != null)) {
+            sq.setStart(start.intValue());
+            sq.setEnd(end.intValue());
+        }
+
+        if (sfeatures != null) {
+            sq.setSequenceFeatures(sfeatures);
+        }
+
+        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);
+    }
+
+    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];
+
+        if (!write_names) {
+            for (int i = 0; i < sequences.length; i++) {
+                String safename = new String("Sequence" + i);
+                map.put(safename, SeqCharacterHash(sequences[i]));
+
+                if (write_names) {
+                    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())) {
+                Hashtable sqinfo = (Hashtable) map.get(sequences[i].getName());
+                SeqCharacterUnhash(sequences[i], sqinfo);
+            } else {
+                allfound = false;
+            }
+        }
+
+        return allfound;
+    }
+}