-/*
-* 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
-*/
-
-package jalview.datamodel;
-
-import java.util.*;
-
-/**
- * <p>Title: </p>
- *
- * <p>Description: </p>
- *
- * <p>Copyright: Copyright (c) 2004</p>
- *
- * <p>Company: Dundee University</p>
- *
- * @author not attributable
- * @version 1.0
- */
-public class AlignmentOrder
-{
- public AlignmentOrder()
- {
- }
-
- public void setType(int Type)
- {
- this.Type = Type;
- }
-
- public int getType()
- {
- return Type;
- }
-
- public void setName(String Name)
- {
- this.Name = Name;
- }
-
- public String getName()
- {
- return Name;
- }
-
- public void setOrder(Vector Order)
- {
- this.Order = Order;
- }
-
- public Vector getOrder()
- {
-
- return Order;
- }
-// JBPNote : this method would return a vector containing all sequences in seqset
-// with those also contained in order at the beginning of the vector in the order
-// given by order. AlignmentSorter.vectorSubsetToArray already does this, but that method
-// should be here for completeness.
-
-/* 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;
- }
- */
- public static final int FILE = 0;
- public static final int MSA = 1;
- public static final int USER = 2;
-
- private int Type = 0;
- private String Name;
- private Vector Order = null;
-
- /**
- * AlignmentOrder
- *
- * @param anOrder Vector
- */
- public AlignmentOrder(Vector anOrder)
- {
- Order = anOrder;
- }
-
- /**
- * AlignmentOrder
- *
- * @param orderFrom AlignmentI
- */
- public AlignmentOrder(AlignmentI orderFrom)
- {
- Order = new Vector();
-
- for (int i=0,ns=orderFrom.getHeight(); i<ns; i++)
- Order.addElement(orderFrom.getSequenceAt(i));
- }
- public AlignmentOrder(SequenceI[] orderFrom) {
- Order = new Vector();
- for (int i=0,ns=orderFrom.length; i<ns; i++)
- Order.addElement(orderFrom[i]);
- }
-
-
-
- /**
- * AlignmentOrder
- *
- * @param orderThis AlignmentI
- * @param byThat AlignmentI
- */
- /* 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
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2007 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>\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
+{\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)\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
+ /**\r
+ * Creates a new AlignmentOrder object.\r
+ */\r
+ public AlignmentOrder()\r
+ {\r
+ }\r
+\r
+ /**\r
+ * AlignmentOrder\r
+ *\r
+ * @param anOrder Vector\r
+ */\r
+ public AlignmentOrder(Vector anOrder)\r
+ {\r
+ Order = anOrder;\r
+ }\r
+\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
+ /**\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
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param Type DOCUMENT ME!\r
+ */\r
+ public void setType(int Type)\r
+ {\r
+ this.Type = Type;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int getType()\r
+ {\r
+ return Type;\r
+ }\r
+\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
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String getName()\r
+ {\r
+ return Name;\r
+ }\r
+\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
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public Vector getOrder()\r
+ {\r
+ return Order;\r
+ }\r
+\r
+ /**\r
+ * replaces oldref with newref in the alignment order.\r
+ * @param oldref\r
+ * @param newref\r
+ * @return true if oldref was contained in order and replaced with newref\r
+ */\r
+ public boolean updateSequence(SequenceI oldref, SequenceI newref)\r
+ {\r
+ int found = Order.indexOf(oldref);\r
+ if (found > -1)\r
+ {\r
+ Order.setElementAt(newref, found);\r
+ }\r
+ return found > -1;\r
+ }\r
+\r
+ /**\r
+ * Exact equivalence of two AlignmentOrders\r
+ * @param o\r
+ * @return true if o orders the same sequenceI objects in the same way\r
+ */\r
+ public boolean equals(AlignmentOrder o)\r
+ {\r
+ return equals(o, true);\r
+ }\r
+\r
+ /**\r
+ * Exact equivalence of two AlignmentOrders\r
+ * // TODO: Weak SequenceI equivalence - will throw Error at moment\r
+ * @param o\r
+ * @param identity - false - use weak equivalence (refers to same or different parts of same sequence)\r
+ * @return true if o orders equivalent sequenceI objects in the same way\r
+ */\r
+ public boolean equals(AlignmentOrder o, boolean identity)\r
+ {\r
+ if (o != this)\r
+ {\r
+ if (o == null)\r
+ {\r
+ return false;\r
+ }\r
+ if (Order != null && o.Order != null && Order.size() == o.Order.size())\r
+ {\r
+ if (!identity)\r
+ {\r
+ throw new Error("Weak sequenceI equivalence not yet implemented.");\r
+ }\r
+ else\r
+ {\r
+ for (int i = 0, j = o.Order.size(); i < j; i++)\r
+ {\r
+ if (Order.elementAt(i) != o.Order.elementAt(i))\r
+ {\r
+ return false;\r
+ }\r
+ }\r
+ }\r
+ }\r
+ else\r
+ {\r
+ return false;\r
+ }\r
+ }\r
+ return true;\r
+ }\r
+\r
+ /**\r
+ * Consistency test for alignmentOrders\r
+ * @param o\r
+ * @return true if o contains or is contained by this and the common SequenceI objects are ordered in the same way\r
+ */\r
+ public boolean isConsistent(AlignmentOrder o)\r
+ {\r
+ return isConsistent(o, true);\r
+ }\r
+\r
+ /**\r
+ * Consistency test for alignmentOrders\r
+ * @param o\r
+ * // TODO: Weak SequenceI equivalence - will throw Error at moment\r
+ * @param identity - false - use weak equivalence (refers to same or different parts of same sequence)\r
+ * @return true if o contains or is contained by this and the common SequenceI objects are ordered in the same way\r
+ */\r
+ public boolean isConsistent(AlignmentOrder o, boolean identity)\r
+ {\r
+ if (o != this)\r
+ {\r
+ if (o == null)\r
+ {\r
+ return false;\r
+ }\r
+ if (Order != null && o.Order != null)\r
+ {\r
+ Vector c, s;\r
+ if (o.Order.size() > Order.size())\r
+ {\r
+ c = o.Order;\r
+ s = Order;\r
+ }\r
+ else\r
+ {\r
+ c = Order;\r
+ s = o.Order;\r
+ }\r
+ if (!identity)\r
+ {\r
+ throw new Error("Weak sequenceI equivalence not yet implemented.");\r
+ }\r
+ else\r
+ {\r
+ // test if c contains s and order in s is conserved in c\r
+ int last = -1;\r
+ for (int i = 0, j = s.size(); i < j; i++)\r
+ {\r
+ int pos = c.indexOf(s.elementAt(i)); // JBPNote - optimize by incremental position search\r
+ if (pos > last)\r
+ {\r
+ last = pos;\r
+ }\r
+ else\r
+ {\r
+ return false;\r
+ }\r
+ }\r
+ }\r
+ }\r
+ else\r
+ {\r
+ return false;\r
+ }\r
+ }\r
+ return true;\r
+ }\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
+ } */\r
+}\r
git://source.jalview.org / jalview.git / blobdiff