-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * 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
-package jalview.datamodel;\r
-\r
-import java.awt.*;\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class SequenceNode extends BinaryNode\r
-{\r
- /** DOCUMENT ME!! */\r
- public float dist;\r
-\r
- /** DOCUMENT ME!! */\r
- public int count;\r
-\r
- /** DOCUMENT ME!! */\r
- public float height;\r
-\r
- /** DOCUMENT ME!! */\r
- public float ycount;\r
-\r
- /** DOCUMENT ME!! */\r
- public Color color = Color.black;\r
-\r
- /** DOCUMENT ME!! */\r
- public boolean dummy = false;\r
- private boolean placeholder = false;\r
-\r
- /**\r
- * Creates a new SequenceNode object.\r
- */\r
- public SequenceNode()\r
- {\r
- super();\r
- }\r
-\r
- /**\r
- * Creates a new SequenceNode object.\r
- *\r
- * @param val DOCUMENT ME!\r
- * @param parent DOCUMENT ME!\r
- * @param dist DOCUMENT ME!\r
- * @param name DOCUMENT ME!\r
- */\r
- public SequenceNode(Object val, SequenceNode parent, float dist, String name)\r
- {\r
- super(val, parent, name);\r
- this.dist = dist;\r
- }\r
-\r
- /**\r
- * Creates a new SequenceNode object.\r
- *\r
- * @param val DOCUMENT ME!\r
- * @param parent DOCUMENT ME!\r
- * @param name DOCUMENT ME!\r
- * @param dist DOCUMENT ME!\r
- * @param bootstrap DOCUMENT ME!\r
- * @param dummy DOCUMENT ME!\r
- */\r
- public SequenceNode(Object val, SequenceNode parent, String name,\r
- float dist, int bootstrap, boolean dummy)\r
- {\r
- super(val, parent, name);\r
- this.dist = dist;\r
- this.bootstrap = bootstrap;\r
- this.dummy = dummy;\r
- }\r
-\r
- /**\r
- * @param dummy true if node is created for the representation of polytomous trees\r
- */\r
- public boolean isDummy()\r
- {\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
- {\r
- return placeholder;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param newstate DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public boolean setDummy(boolean newstate)\r
- {\r
- boolean oldstate = dummy;\r
- dummy = newstate;\r
-\r
- return oldstate;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param Placeholder DOCUMENT ME!\r
- */\r
- public void setPlaceholder(boolean Placeholder)\r
- {\r
- this.placeholder = Placeholder;\r
- }\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
- {\r
- SequenceNode c = this;\r
-\r
- do\r
- {\r
- c = (SequenceNode) c.parent();\r
- }\r
- while ((c != null) && c.dummy);\r
-\r
- return c;\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+ */
+package jalview.datamodel;
+
+import java.awt.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class SequenceNode extends BinaryNode
+{
+ /** 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;
+
+ /**
+ * Creates a new SequenceNode object.
+ */
+ public SequenceNode()
+ {
+ 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)
+ {
+ 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!
+ */
+ public SequenceNode(Object val, SequenceNode parent, String name,
+ float dist, int bootstrap, boolean dummy)
+ {
+ super(val, parent, name);
+ this.dist = dist;
+ this.bootstrap = bootstrap;
+ this.dummy = dummy;
+ }
+
+ /**
+ * @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
+ */
+ public boolean isPlaceholder()
+ {
+ return placeholder;
+ }
+
+ /**
+ * 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!
+ */
+ public void setPlaceholder(boolean Placeholder)
+ {
+ this.placeholder = 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
+ *
+ * @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;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff