-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 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
-* 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.
-*
-* 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
-*/\r
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 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.util.*;\r
\r
\r
-/**
- * <p>Title: </p>
- *
- * <p>Description: </p>
- *
- * <p>Copyright: Copyright (c) 2004</p>
- *
- * <p>Company: Dundee University</p>
- *
- * @author not attributable
- * @version 1.0
+/**\r
+ * <p>Title: </p>\r
+ *\r
+ * <p>Description: </p>\r
+ *\r
+ * <p>Copyright: Copyright (c) 2004</p>\r
+ *\r
+ * <p>Company: Dundee University</p>\r
+ *\r
+ * @author not attributable\r
+ * @version 1.0\r
*/\r
-public class AlignmentOrder {\r
+public class AlignmentOrder\r
+{\r
// JBPNote : this method would return a vector containing all sequences in seqset\r
// with those also contained in order at the beginning of the vector in the order\r
// given by order. AlignmentSorter.vectorSubsetToArray already does this, but that method\r
// should be here for completeness.\r
\r
- /* public Vector getOrder(AlignmentI seqset)
- {
- Vector perm = new Vector(seqset.getHeight());
- for (i=0, o = 0, n=seqset.getHeight(), p = Order.size(); i<n; i++)
- perm.setElement(i,...).
- return Order;
- }
- */\r
+ /* public Vector getOrder(AlignmentI seqset)\r
+ {\r
+ Vector perm = new Vector(seqset.getHeight());\r
+ for (i=0, o = 0, n=seqset.getHeight(), p = Order.size(); i<n; i++)\r
+ perm.setElement(i,...).\r
+ return Order;\r
+ }\r
+ */\r
+\r
+ /** DOCUMENT ME!! */\r
public static final int FILE = 0;\r
+\r
+ /** DOCUMENT ME!! */\r
public static final int MSA = 1;\r
+\r
+ /** DOCUMENT ME!! */\r
public static final int USER = 2;\r
private int Type = 0;\r
private String Name;\r
private Vector Order = null;\r
\r
- public AlignmentOrder() {\r
+ /**\r
+ * Creates a new AlignmentOrder object.\r
+ */\r
+ public AlignmentOrder()\r
+ {\r
}\r
\r
- /**
- * AlignmentOrder
- *
- * @param anOrder Vector
- */\r
- public AlignmentOrder(Vector anOrder) {\r
+ /**\r
+ * AlignmentOrder\r
+ *\r
+ * @param anOrder Vector\r
+ */\r
+ public AlignmentOrder(Vector anOrder)\r
+ {\r
Order = anOrder;\r
}\r
\r
- /**
- * AlignmentOrder
- *
- * @param orderFrom AlignmentI
- */\r
- public AlignmentOrder(AlignmentI orderFrom) {\r
+ /**\r
+ * AlignmentOrder\r
+ *\r
+ * @param orderFrom AlignmentI\r
+ */\r
+ public AlignmentOrder(AlignmentI orderFrom)\r
+ {\r
Order = new Vector();\r
\r
for (int i = 0, ns = orderFrom.getHeight(); i < ns; i++)\r
+ {\r
Order.addElement(orderFrom.getSequenceAt(i));\r
+ }\r
}\r
\r
- public AlignmentOrder(SequenceI[] orderFrom) {\r
+ /**\r
+ * Creates a new AlignmentOrder object.\r
+ *\r
+ * @param orderFrom DOCUMENT ME!\r
+ */\r
+ public AlignmentOrder(SequenceI[] orderFrom)\r
+ {\r
Order = new Vector();\r
\r
for (int i = 0, ns = orderFrom.length; i < ns; i++)\r
+ {\r
Order.addElement(orderFrom[i]);\r
+ }\r
}\r
\r
- public void setType(int Type) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param Type DOCUMENT ME!\r
+ */\r
+ public void setType(int Type)\r
+ {\r
this.Type = Type;\r
}\r
\r
- public int getType() {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int getType()\r
+ {\r
return Type;\r
}\r
\r
- public void setName(String Name) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param Name DOCUMENT ME!\r
+ */\r
+ public void setName(String Name)\r
+ {\r
this.Name = Name;\r
}\r
\r
- public String getName() {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String getName()\r
+ {\r
return Name;\r
}\r
\r
- public void setOrder(Vector Order) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param Order DOCUMENT ME!\r
+ */\r
+ public void setOrder(Vector Order)\r
+ {\r
this.Order = Order;\r
}\r
\r
- public Vector getOrder() {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public Vector getOrder()\r
+ {\r
return Order;\r
}\r
\r
- /**
- * AlignmentOrder
- *
- * @param orderThis AlignmentI
- * @param byThat AlignmentI
- */\r
+ /**\r
+ * AlignmentOrder\r
+ *\r
+ * @param orderThis AlignmentI\r
+ * @param byThat AlignmentI\r
+ */\r
+\r
+ /* public AlignmentOrder(AlignmentI orderThis, AlignmentI byThat)\r
+ {\r
+ // Vector is an ordering of this alignment using the order of sequence objects in byThat,\r
+ // where ids and unaligned sequences must match\r
\r
- /* public AlignmentOrder(AlignmentI orderThis, AlignmentI byThat)
-{
- // Vector is an ordering of this alignment using the order of sequence objects in byThat,
- // where ids and unaligned sequences must match
-
-} */\r
+ } */\r
}\r
git://source.jalview.org / jalview.git / blobdiff