Formatted source

[jalview.git] / src / jalview / datamodel / SequenceNode.java

diff --git a/src/jalview/datamodel/SequenceNode.java b/src/jalview/datamodel/SequenceNode.java
index 74776ea..f86c63e 100755 (executable)
--- a/src/jalview/datamodel/SequenceNode.java
+++ b/src/jalview/datamodel/SequenceNode.java
@@ -16,73 +16,73 @@
 * along with this program; if not, write to the Free Software\r
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
 */\r
-\r
 package jalview.datamodel;\r
 \r
 import java.awt.*;\r
 \r
+\r
 public class SequenceNode extends BinaryNode {\r
+    public float dist;\r
+    public int count;\r
+    public float height;\r
+    public float ycount;\r
+    public Color color = Color.black;\r
+    public boolean dummy = false;\r
+    private boolean placeholder = false;\r
+\r
+    public SequenceNode() {\r
+        super();\r
+    }\r
 \r
-  public float dist;\r
-  public int count;\r
-  public float height;\r
-  public float ycount;\r
-  public Color color = Color.black;\r
-  public boolean dummy = false;\r
-  private boolean placeholder = false;\r
+    public SequenceNode(Object val, SequenceNode parent, float dist, String name) {\r
+        super(val, parent, name);\r
+        this.dist = dist;\r
+    }\r
 \r
-  public SequenceNode() {\r
-    super();\r
-  }\r
+    public SequenceNode(Object val, SequenceNode parent, String name,\r
+        float dist, int bootstrap, boolean dummy) {\r
+        super(val, parent, name);\r
+        this.dist = dist;\r
+        this.bootstrap = bootstrap;\r
+        this.dummy = dummy;\r
+    }\r
 \r
-  public SequenceNode(Object val, SequenceNode parent, float dist,String name) {\r
-    super(val,parent,name);\r
-    this.dist = dist;\r
-  }\r
-  public SequenceNode(Object val, SequenceNode parent, String name, float dist, int bootstrap, boolean dummy) {\r
-    super(val,parent,name);\r
-    this.dist = dist;\r
-    this.bootstrap = bootstrap;\r
-    this.dummy = dummy;\r
-  }\r
+    /**\r
+     * @param dummy true if node is created for the representation of polytomous trees\r
+     */\r
+    public boolean isDummy() {\r
+        return dummy;\r
+    }\r
 \r
+    /* @param placeholder is true if the sequence refered to in the\r
+     *  element node is not actually present in the associated alignment\r
+     */\r
+    public boolean isPlaceholder() {\r
+        return placeholder;\r
+    }\r
 \r
-  /**\r
-   * @param dummy true if node is created for the representation of polytomous trees\r
-   */\r
+    public boolean setDummy(boolean newstate) {\r
+        boolean oldstate = dummy;\r
+        dummy = newstate;\r
 \r
-  public boolean isDummy() {\r
-    return dummy;\r
-  }\r
-  /* @param placeholder is true if the sequence refered to in the\r
-   *  element node is not actually present in the associated alignment\r
-   */\r
-  public boolean isPlaceholder()\r
-  {\r
-    return placeholder;\r
-  }\r
+        return oldstate;\r
+    }\r
 \r
-  public boolean setDummy(boolean newstate) {\r
-    boolean oldstate = dummy;\r
-    dummy = newstate;\r
-    return oldstate;\r
-  }\r
+    public void setPlaceholder(boolean Placeholder) {\r
+        this.placeholder = Placeholder;\r
+    }\r
 \r
-  public void setPlaceholder(boolean Placeholder)\r
-  {\r
-    this.placeholder = Placeholder;\r
-  }\r
+    /**\r
+     * ascends the tree but doesn't stop until a non-dummy node is discovered.\r
+     * This will probably break if the tree is a mixture of BinaryNodes and SequenceNodes.\r
+     */\r
+    public SequenceNode AscendTree() {\r
+        SequenceNode c = this;\r
 \r
-  /**\r
-   * ascends the tree but doesn't stop until a non-dummy node is discovered.\r
-   * This will probably break if the tree is a mixture of BinaryNodes and SequenceNodes.\r
-   */\r
+        do {\r
+            c = (SequenceNode) c.parent();\r
+        } while ((c != null) && c.dummy);\r
 \r
-  public SequenceNode AscendTree() {\r
-    SequenceNode c = this;\r
-    do {\r
-      c = (SequenceNode) c.parent();\r
-    } while (c!=null && c.dummy);\r
-    return c;\r
-  }\r
+        return c;\r
+    }\r
 }\r