-/*
- * 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
-{
- // 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;
- }
- */
-
- /** DOCUMENT ME!! */
- public static final int FILE = 0;
-
- /** DOCUMENT ME!! */
- public static final int MSA = 1;
-
- /** DOCUMENT ME!! */
- public static final int USER = 2;
- private int Type = 0;
- private String Name;
- private Vector Order = null;
-
- /**
- * Creates a new AlignmentOrder object.
- */
- public AlignmentOrder()
- {
- }
-
- /**
- * 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));
- }
- }
-
- /**
- * Creates a new AlignmentOrder object.
- *
- * @param orderFrom DOCUMENT ME!
- */
- public AlignmentOrder(SequenceI[] orderFrom)
- {
- Order = new Vector();
-
- for (int i = 0, ns = orderFrom.length; i < ns; i++)
- {
- Order.addElement(orderFrom[i]);
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param Type DOCUMENT ME!
- */
- public void setType(int Type)
- {
- this.Type = Type;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getType()
- {
- return Type;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param Name DOCUMENT ME!
- */
- public void setName(String Name)
- {
- this.Name = Name;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String getName()
- {
- return Name;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param Order DOCUMENT ME!
- */
- public void setOrder(Vector Order)
- {
- this.Order = Order;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Vector getOrder()
- {
- return Order;
- }
- /**
- * replaces oldref with newref in the alignment order.
- * @param oldref
- * @param newref
- * @return
- */
- public boolean updateSequence(SequenceI oldref, SequenceI newref) {
- int found=Order.indexOf(oldref);
- if (found>-1) {
- Order.setElementAt(newref, found);
- }
- return found>-1;
- }
- /**
- * Exact equivalence of two AlignmentOrders
- * @param o
- * @return true if o orders the same sequenceI objects in the same way
- */
- public boolean equals(AlignmentOrder o) {
- return equals(o, true);
- }
- /**
- * Exact equivalence of two AlignmentOrders
- * // TODO: Weak SequenceI equivalence - will throw Error at moment
- * @param o
- * @param identity - false - use weak equivalence (refers to same or different parts of same sequence)
- * @return true if o orders equivalent sequenceI objects in the same way
- */
- public boolean equals(AlignmentOrder o, boolean identity) {
- if (o!=this) {
- if (o==null)
- return false;
- if (Order!=null && o.Order!=null && Order.size()==o.Order.size()) {
- if (!identity) {
- throw new Error("Weak sequenceI equivalence not yet implemented.");
- } else {
- for (int i=0,j=o.Order.size(); i<j; i++) {
- if (Order.get(i)!=o.Order.get(i))
- return false;
- }
- }
- } else
- return false;
- }
- return true;
- }
- /**
- * Consistency test for alignmentOrders
- * @param o
- * @return true if o contains or is contained by this and the common SequenceI objects are ordered in the same way
- */
- public boolean isConsistent(AlignmentOrder o) {
- return isConsistent(o, true);
- }
- /**
- * Consistency test for alignmentOrders
- * @param o
- * // TODO: Weak SequenceI equivalence - will throw Error at moment
- * @param identity - false - use weak equivalence (refers to same or different parts of same sequence)
- * @return true if o contains or is contained by this and the common SequenceI objects are ordered in the same way
- */
- public boolean isConsistent(AlignmentOrder o, boolean identity) {
- if (o!=this) {
- if (o==null)
- return false;
- if (Order!=null && o.Order!=null) {
- Vector c,s;
- if (o.Order.size()>Order.size()) {
- c = o.Order;
- s = Order;
- } else {
- c = Order;
- s = o.Order;
- }
- if (!identity) {
- throw new Error("Weak sequenceI equivalence not yet implemented.");
- } else {
- // test if c contains s and order in s is conserved in c
- int last=-1;
- for (int i=0,j=s.size(); i<j; i++) {
- int pos=c.indexOf(s.get(i)); // JBPNote - optimize by incremental position search
- if (pos>last) {
- last=pos;
- } else
- return false;
- }
- }
- } else
- return false;
- }
- return true;
- }
- /**
- * 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