Formatted source

[jalview.git] / src / jalview / analysis / SequenceIdMatcher.java

diff --git a/src/jalview/analysis/SequenceIdMatcher.java b/src/jalview/analysis/SequenceIdMatcher.java
index 1c156cd..f786243 100755 (executable)
--- a/src/jalview/analysis/SequenceIdMatcher.java
+++ b/src/jalview/analysis/SequenceIdMatcher.java
@@ -15,14 +15,15 @@
 * 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.Vector;
-import java.util.Hashtable;
-import jalview.datamodel.SequenceI;
-
+*/\r
+package jalview.analysis;\r
+\r
+import jalview.datamodel.SequenceI;\r
+\r
+import java.util.Hashtable;\r
+import java.util.Vector;\r
+\r
+\r
 /**
  * <p>Title: </p>
  * SequenceIdMatcher
@@ -34,123 +35,105 @@ import jalview.datamodel.SequenceI;
  *
  * @author not attributable
  * @version 1.0
- */
-public class SequenceIdMatcher
-{
-
-  private class SeqIdName
-  {
-    String id;
-
-    SeqIdName(String s)
-    {
-      id = new String(s);
-    }
-
-    public int hashCode()
-    {
-      return (id.substring(0, 4).hashCode());
-    }
-
-    public boolean equals(Object s)
-    {
-      if (s instanceof SeqIdName)
-      {
-        return this.equals( (SeqIdName) s);
-      }
-      else
-      {
-        if (s instanceof String)
-        {
-          return this.equals( (String) s);
-        }
-      }
-      return false;
-    }
-
-    public boolean equals(SeqIdName s)
-    {
-      if (id.startsWith(s.id) || s.id.startsWith(id))
-      {
-        return true;
-      }
-      return false;
-    }
-
-    public boolean equals(String s)
-    {
-      if (id.startsWith(s) || s.startsWith(id))
-      {
-        return true;
-      }
-      return false;
-    }
-  }
-
-  private Hashtable names;
-
-  public SequenceIdMatcher(SequenceI[] seqs)
-  {
-    names = new Hashtable();
-    for (int i = 0; i < seqs.length; i++)
-    {
-      names.put(new SeqIdName(seqs[i].getName()), seqs[i]);
-    }
-  }
-
-  SequenceI findIdMatch(SequenceI seq)
-  {
-    SeqIdName nam = new SeqIdName(seq.getName());
-    if (names.containsKey(nam))
-    {
-      return (SequenceI) names.get(nam);
-    }
-    return null;
-  }
-
-  SequenceI findIdMatch(String seqnam)
-  {
-    SeqIdName nam = new SeqIdName(seqnam);
-    if (names.containsKey(nam))
-    {
-      return (SequenceI) names.get(nam);
-    }
-    return null;
-  }
-
-  /**
-   * findIdMatch
-   *
-   * Return pointers to sequences (or sequence object containers)
-   * which have same Id as a given set of different sequence objects
-   *
-   * @param seqs SequenceI[]
-   * @return SequenceI[]
-   */
-
-  SequenceI[] findIdMatch(SequenceI[] seqs)
-  {
-    SequenceI[] namedseqs = new SequenceI[seqs.length];
-
-    int i = 0;
-    SeqIdName nam;
-    if (seqs.length > 0)
-    {
-      do
-      {
-        nam = new SeqIdName(seqs[i].getName());
-        if (names.containsKey(nam))
-        {
-          namedseqs[i] = (SequenceI) names.get(nam);
-        }
-        else
-        {
-          namedseqs[i] = null;
-        }
-      }
-      while (i++ < seqs.length);
-    }
-    return namedseqs;
-  }
-
-}
+ */\r
+public class SequenceIdMatcher {\r
+    private Hashtable names;\r
+\r
+    public SequenceIdMatcher(SequenceI[] seqs) {\r
+        names = new Hashtable();\r
+\r
+        for (int i = 0; i < seqs.length; i++) {\r
+            names.put(new SeqIdName(seqs[i].getName()), seqs[i]);\r
+        }\r
+    }\r
+\r
+    SequenceI findIdMatch(SequenceI seq) {\r
+        SeqIdName nam = new SeqIdName(seq.getName());\r
+\r
+        if (names.containsKey(nam)) {\r
+            return (SequenceI) names.get(nam);\r
+        }\r
+\r
+        return null;\r
+    }\r
+\r
+    SequenceI findIdMatch(String seqnam) {\r
+        SeqIdName nam = new SeqIdName(seqnam);\r
+\r
+        if (names.containsKey(nam)) {\r
+            return (SequenceI) names.get(nam);\r
+        }\r
+\r
+        return null;\r
+    }\r
+\r
+    /**
+ * findIdMatch
+ *
+ * Return pointers to sequences (or sequence object containers)
+ * which have same Id as a given set of different sequence objects
+ *
+ * @param seqs SequenceI[]
+ * @return SequenceI[]
+ */\r
+    SequenceI[] findIdMatch(SequenceI[] seqs) {\r
+        SequenceI[] namedseqs = new SequenceI[seqs.length];\r
+\r
+        int i = 0;\r
+        SeqIdName nam;\r
+\r
+        if (seqs.length > 0) {\r
+            do {\r
+                nam = new SeqIdName(seqs[i].getName());\r
+\r
+                if (names.containsKey(nam)) {\r
+                    namedseqs[i] = (SequenceI) names.get(nam);\r
+                } else {\r
+                    namedseqs[i] = null;\r
+                }\r
+            } while (i++ < seqs.length);\r
+        }\r
+\r
+        return namedseqs;\r
+    }\r
+\r
+    private class SeqIdName {\r
+        String id;\r
+\r
+        SeqIdName(String s) {\r
+            id = new String(s);\r
+        }\r
+\r
+        public int hashCode() {\r
+            return (id.substring(0, 4).hashCode());\r
+        }\r
+\r
+        public boolean equals(Object s) {\r
+            if (s instanceof SeqIdName) {\r
+                return this.equals((SeqIdName) s);\r
+            } else {\r
+                if (s instanceof String) {\r
+                    return this.equals((String) s);\r
+                }\r
+            }\r
+\r
+            return false;\r
+        }\r
+\r
+        public boolean equals(SeqIdName s) {\r
+            if (id.startsWith(s.id) || s.id.startsWith(id)) {\r
+                return true;\r
+            }\r
+\r
+            return false;\r
+        }\r
+\r
+        public boolean equals(String s) {\r
+            if (id.startsWith(s) || s.startsWith(id)) {\r
+                return true;\r
+            }\r
+\r
+            return false;\r
+        }\r
+    }\r
+}\r