/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, 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
+ * 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.
- *
- * 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 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
-import java.awt.*;
-
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
-public class SequenceNode
- extends BinaryNode
+public class SequenceNode extends BinaryNode<SequenceI>
{
- /** DOCUMENT ME!! */
- public float dist;
-
- /** DOCUMENT ME!! */
- public int count;
-
- /** DOCUMENT ME!! */
- public float height;
-
- /** DOCUMENT ME!! */
- public float ycount;
-
- /** DOCUMENT ME!! */
- public Color color = Color.black;
-
- /** DOCUMENT ME!! */
- public boolean dummy = false;
private boolean placeholder = false;
/**
super();
}
- /**
- * Creates a new SequenceNode object.
- *
- * @param val DOCUMENT ME!
- * @param parent DOCUMENT ME!
- * @param dist DOCUMENT ME!
- * @param name DOCUMENT ME!
- */
- public SequenceNode(Object val, SequenceNode parent, float dist, String name)
+ public SequenceNode(SequenceI val, BinaryNode<SequenceI> parent,
+ String name, double dist, int bootstrap, boolean dummy)
{
- super(val, parent, name);
- this.dist = dist;
+ super(val, parent, name, dist, bootstrap, dummy);
}
- /**
- * Creates a new SequenceNode object.
- *
- * @param val DOCUMENT ME!
- * @param parent DOCUMENT ME!
- * @param name DOCUMENT ME!
- * @param dist DOCUMENT ME!
- * @param bootstrap DOCUMENT ME!
- * @param dummy DOCUMENT ME!
- */
- public SequenceNode(Object val, SequenceNode parent, String name,
- float dist, int bootstrap, boolean dummy)
+ public SequenceNode(SequenceI element, BinaryNode<SequenceI> parent,
+ String name, double dist, int bootstrap)
{
- super(val, parent, name);
- this.dist = dist;
- this.bootstrap = bootstrap;
- this.dummy = dummy;
+ super(element, parent, name, dist, bootstrap);
}
- /**
- * @param dummy true if node is created for the representation of polytomous trees
- */
- public boolean isDummy()
+ public SequenceNode(SequenceI element, BinaryNode<SequenceI> parent,
+ String name, double dist)
{
- return dummy;
+ 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
+ /*
+ * @param placeholder is true if the sequence refered to in the element node
+ * is not actually present in the associated alignment
*/
public boolean isPlaceholder()
{
/**
* DOCUMENT ME!
- *
- * @param newstate DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean setDummy(boolean newstate)
- {
- boolean oldstate = dummy;
- dummy = newstate;
-
- return oldstate;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param Placeholder DOCUMENT ME!
+ *
+ * @param Placeholder
+ * DOCUMENT ME!
*/
public void setPlaceholder(boolean Placeholder)
{
}
/**
- * ascends the tree but doesn't stop until a non-dummy node is discovered.
- * This will probably break if the tree is a mixture of BinaryNodes and SequenceNodes.
- */
- public SequenceNode AscendTree()
- {
- SequenceNode c = this;
-
- do
- {
- c = (SequenceNode) c.parent();
- }
- while ( (c != null) && c.dummy);
-
- return c;
- }
- /**
- * test if this node has a name that might be a label rather than a bootstrap value
+ * 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)
+ if (name != null && name.length() > 0)
{
- for (int c=0,s=name.length(); c<s; c++)
+ for (int c = 0, s = name.length(); c < s; c++)
{
char q = name.charAt(c);
- if ('0'<=q && q<='9')
+ if ('0' <= q && q <= '9')
+ {
continue;
+ }
return true;
}
}
git://source.jalview.org / jalview.git / blobdiff