/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\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
\r
import java.util.*;\r
\r
-\r
/**\r
* <p>Title: </p>\r
*\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
+ // 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
+ /* 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
+ /** DOCUMENT ME!! */\r
+ public static final int FILE = 0;\r
\r
- /** DOCUMENT ME!! */\r
- public static final int MSA = 1;\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
+ /** 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
+ * 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
+ * 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 = anOrder;\r
+ Order.addElement(orderFrom.getSequenceAt(i));\r
}\r
+ }\r
\r
- /**\r
- * AlignmentOrder\r
- *\r
- * @param orderFrom AlignmentI\r
- */\r
- public AlignmentOrder(AlignmentI orderFrom)\r
- {\r
- Order = new Vector();\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.getHeight(); i < ns; i++)\r
- {\r
- Order.addElement(orderFrom.getSequenceAt(i));\r
- }\r
+ for (int i = 0, ns = orderFrom.length; i < ns; i++)\r
+ {\r
+ Order.addElement(orderFrom[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
+ * DOCUMENT ME!\r
+ *\r
+ * @param Type DOCUMENT ME!\r
+ */\r
+ public void setType(int Type)\r
+ {\r
+ this.Type = Type;\r
+ }\r
\r
- for (int i = 0, ns = orderFrom.length; i < ns; i++)\r
- {\r
- Order.addElement(orderFrom[i]);\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 Type DOCUMENT ME!\r
- */\r
- public void setType(int Type)\r
- {\r
- this.Type = Type;\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 int getType()\r
- {\r
- return Type;\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 Name DOCUMENT ME!\r
- */\r
- public void setName(String Name)\r
- {\r
- this.Name = Name;\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 String getName()\r
- {\r
- return Name;\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public Vector getOrder()\r
+ {\r
+ return Order;\r
+ }\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param Order DOCUMENT ME!\r
- */\r
- public void setOrder(Vector Order)\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
- this.Order = Order;\r
+ Order.setElementAt(newref, found);\r
}\r
+ return found > -1;\r
+ }\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public Vector getOrder()\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
- return Order;\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
- int found=Order.indexOf(oldref);\r
- if (found>-1) {\r
- Order.setElementAt(newref, found);\r
+ if (o == null)\r
+ {\r
+ return false;\r
}\r
- return found>-1;\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
- return equals(o, true);\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
- if (o!=this) {\r
- if (o==null)\r
- return false;\r
- if (Order!=null && o.Order!=null && Order.size()==o.Order.size()) {\r
- if (!identity) {\r
- throw new Error("Weak sequenceI equivalence not yet implemented.");\r
- } else {\r
- for (int i=0,j=o.Order.size(); i<j; i++) {\r
- if (Order.elementAt(i)!=o.Order.elementAt(i))\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
- } else\r
- return false;\r
+ }\r
+ }\r
+ else\r
+ {\r
+ return false;\r
}\r
- return true;\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
- return isConsistent(o, true);\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
- if (o!=this) {\r
- if (o==null)\r
- return false;\r
- if (Order!=null && o.Order!=null) {\r
- Vector c,s;\r
- if (o.Order.size()>Order.size()) {\r
- c = o.Order;\r
- s = Order;\r
- } else {\r
- c = Order;\r
- s = o.Order;\r
- }\r
- if (!identity) {\r
- throw new Error("Weak sequenceI equivalence not yet implemented.");\r
- } else {\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
- int pos=c.indexOf(s.elementAt(i)); // JBPNote - optimize by incremental position search\r
- if (pos>last) {\r
- last=pos;\r
- } else\r
- return false;\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
- } else\r
- return false;\r
+ }\r
+ }\r
+ else\r
+ {\r
+ return false;\r
}\r
- return true;\r
}\r
- /**\r
- * AlignmentOrder\r
- *\r
- * @param orderThis AlignmentI\r
- * @param byThat AlignmentI\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
+ /* 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
}\r
git://source.jalview.org / jalview.git / blobdiff