-package jalview.datamodel;\r
-\r
-import java.awt.Color;\r
-\r
-public class SequenceNode extends BinaryNode {\r
-\r
- public float dist;\r
- public int count;\r
- public float height;\r
- public float ycount;\r
- public Color color = Color.black;\r
-\r
- public SequenceNode() {\r
- super();\r
- }\r
- \r
- public SequenceNode(Object val, SequenceNode parent, float dist,String name) {\r
- super(val,parent,name);\r
- this.dist = dist;\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * 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.
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.datamodel;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class SequenceNode extends BinaryNode<SequenceI>
+{
+ private boolean placeholder = false;
+
+ /**
+ * Creates a new SequenceNode object.
+ */
+ public SequenceNode()
+ {
+ super();
+ }
+
+ public SequenceNode(SequenceI val, BinaryNode<SequenceI> parent,
+ String name, double dist, int bootstrap, boolean dummy)
+ {
+ super(val, parent, name, dist, bootstrap, dummy);
+ }
+
+ public SequenceNode(SequenceI element, BinaryNode<SequenceI> parent,
+ String name, double dist, int bootstrap)
+ {
+ super(element, parent, name, dist, bootstrap);
+ }
+
+ public SequenceNode(SequenceI element, BinaryNode<SequenceI> parent,
+ String name, double dist)
+ {
+ super(element, parent, name, dist);
+ }
+
+ /*
+ * @param placeholder is true if the sequence refered to in the element node
+ * is not actually present in the associated alignment
+ */
+ public boolean isPlaceholder()
+ {
+ return placeholder;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param Placeholder
+ * DOCUMENT ME!
+ */
+ public void setPlaceholder(boolean Placeholder)
+ {
+ this.placeholder = Placeholder;
+ }
+
+ /**
+ * test if this node has a name that might be a label rather than a bootstrap
+ * value
+ *
+ * @return true if node has a non-numeric label
+ */
+ public boolean isSequenceLabel()
+ {
+ if (name != null && name.length() > 0)
+ {
+ for (int c = 0, s = name.length(); c < s; c++)
+ {
+ char q = name.charAt(c);
+ if ('0' <= q && q <= '9')
+ {
+ continue;
+ }
+ return true;
+ }
+ }
+ return false;
+ }
+}