/*
- * 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.*;
+import java.awt.Color;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
-public class SequenceNode
- extends BinaryNode
+public class SequenceNode extends BinaryNode
{
/** DOCUMENT ME!! */
- public float dist;
+ public double dist;
/** DOCUMENT ME!! */
public int count;
/** DOCUMENT ME!! */
- public float height;
+ public double height;
/** DOCUMENT ME!! */
public float ycount;
/** DOCUMENT ME!! */
public boolean dummy = false;
+
private boolean placeholder = false;
/**
/**
* Creates a new SequenceNode object.
- *
- * @param val DOCUMENT ME!
- * @param parent DOCUMENT ME!
- * @param dist DOCUMENT ME!
- * @param name DOCUMENT ME!
+ *
+ * @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(Object val, SequenceNode parent, float dist,
+ String name)
{
super(val, parent, name);
this.dist = dist;
/**
* 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!
+ *
+ * @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)
+ float dist, int bootstrap, boolean dummy)
{
super(val, parent, name);
this.dist = dist;
}
/**
- * @param dummy true if node is created for the representation of polytomous trees
+ * @param dummy
+ * true if node is created for the representation of polytomous trees
*/
public boolean isDummy()
{
return dummy;
}
- /* @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!
- *
+ *
+ * @param newstate
+ * DOCUMENT ME!
+ *
* @return DOCUMENT ME!
*/
public boolean setDummy(boolean newstate)
/**
* 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.
+ * This will probably break if the tree is a mixture of BinaryNodes and
+ * SequenceNodes.
*/
public SequenceNode AscendTree()
{
do
{
c = (SequenceNode) c.parent();
- }
- while ( (c != null) && c.dummy);
+ } 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;
}
}