X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentOrder.java;h=67fc2c3255f6940f7b57dde2241868b1af75786e;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=b14974948a40a1ecb8d03515a3335a93ce773846;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git
diff --git a/src/jalview/datamodel/AlignmentOrder.java b/src/jalview/datamodel/AlignmentOrder.java
index b149749..67fc2c3 100755
--- a/src/jalview/datamodel/AlignmentOrder.java
+++ b/src/jalview/datamodel/AlignmentOrder.java
@@ -1,316 +1,330 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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.*;
-
-/**
- * Title:
- *
- * Description:
- *
- * Copyright: Copyright (c) 2004
- *
- * Company: Dundee University
- *
- * @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 -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.elementAt(i) != o.Order.elementAt(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.elementAt(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
-
- } */
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.datamodel;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+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 Order = null;
+
+ /**
+ * Creates a new AlignmentOrder object.
+ */
+ public AlignmentOrder()
+ {
+ }
+
+ /**
+ * AlignmentOrder
+ *
+ * @param anOrder
+ */
+ public AlignmentOrder(List anOrder)
+ {
+ Order = anOrder;
+ }
+
+ /**
+ * AlignmentOrder
+ *
+ * @param orderFrom
+ * AlignmentI
+ */
+ public AlignmentOrder(AlignmentI orderFrom)
+ {
+ Order = new ArrayList();
+
+ for (SequenceI seq : orderFrom.getSequences())
+ {
+ Order.add(seq);
+ }
+ }
+
+ /**
+ * Creates a new AlignmentOrder object.
+ *
+ * @param orderFrom
+ * DOCUMENT ME!
+ */
+ public AlignmentOrder(SequenceI[] orderFrom)
+ {
+ Order = new ArrayList(Arrays.asList(orderFrom));
+ }
+
+ /**
+ * 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(List Order)
+ {
+ this.Order = Order;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public List getOrder()
+ {
+ return Order;
+ }
+
+ /**
+ * replaces oldref with newref in the alignment order.
+ *
+ * @param oldref
+ * @param newref
+ * @return true if oldref was contained in order and replaced with newref
+ */
+ public boolean updateSequence(SequenceI oldref, SequenceI newref)
+ {
+ int found = Order.indexOf(oldref);
+ if (found > -1)
+ {
+ Order.set(found, newref);
+ }
+ return found > -1;
+ }
+
+ /**
+ * Exact equivalence of two AlignmentOrders
+ *
+ * @param o
+ * @return true if o orders the same sequenceI objects in the same way
+ */
+ @Override
+ public boolean equals(Object o)
+ {
+ if (o == null || !(o instanceof AlignmentOrder))
+ {
+ return false;
+ }
+ return equals((AlignmentOrder) 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)
+ {
+ List 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 }
+ */
+}