X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=ea8d4e58ae553a30a08b5120eba51d40ef6bd9cf;hb=1a0f6886ffdb431de180af2089db4910a1dfb564;hp=778142c24fed58fc045634860caf4029f5be35ee;hpb=0452450533728e478ef8c893ea2cb3483c740fb3;p=jalview.git
diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 778142c..ea8d4e5 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -1,483 +1,486 @@
/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 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
-*/
+ * 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.analysis;
-import jalview.datamodel.*;
-
-import jalview.util.*;
-
import java.util.*;
+import jalview.datamodel.*;
+import jalview.util.*;
/** Data structure to hold and manipulate a multiple sequence alignment
*/
public class AlignmentSorter
{
- static boolean sortIdAscending = true;
- static int lastGroupHash = 0;
- static boolean sortGroupAscending = true;
- static AlignmentOrder lastOrder = null;
- static boolean sortOrderAscending = true;
- static NJTree lastTree = null;
- static boolean sortTreeAscending = true;
-
- /**
- * Sort by Percentage Identity
- *
- * @param align AlignmentI
- * @param s SequenceI
- */
- public static void sortByPID(AlignmentI align, SequenceI s)
- {
- int nSeq = align.getHeight();
-
- float[] scores = new float[nSeq];
- SequenceI[] seqs = new SequenceI[nSeq];
-
- for (int i = 0; i < nSeq; i++)
- {
- scores[i] = Comparison.PID(align.getSequenceAt(i).getSequenceAsString(),
- s.getSequenceAsString());
- seqs[i] = align.getSequenceAt(i);
- }
-
- QuickSort.sort(scores, 0, scores.length - 1, seqs);
-
- setReverseOrder(align, seqs);
+ static boolean sortIdAscending = true;
+ static int lastGroupHash = 0;
+ static boolean sortGroupAscending = true;
+ static AlignmentOrder lastOrder = null;
+ static boolean sortOrderAscending = true;
+ static NJTree lastTree = null;
+ static boolean sortTreeAscending = true;
+
+ /**
+ * Sort by Percentage Identity
+ *
+ * @param align AlignmentI
+ * @param s SequenceI
+ */
+ public static void sortByPID(AlignmentI align, SequenceI s)
+ {
+ int nSeq = align.getHeight();
+
+ float[] scores = new float[nSeq];
+ SequenceI[] seqs = new SequenceI[nSeq];
+
+ for (int i = 0; i < nSeq; i++)
+ {
+ scores[i] = Comparison.PID(align.getSequenceAt(i).getSequenceAsString(),
+ s.getSequenceAsString());
+ seqs[i] = align.getSequenceAt(i);
}
- /**
- * Reverse the order of the sort
- *
- * @param align DOCUMENT ME!
- * @param seqs DOCUMENT ME!
- */
- private static void setReverseOrder(AlignmentI align, SequenceI[] seqs)
- {
- int nSeq = seqs.length;
+ QuickSort.sort(scores, 0, scores.length - 1, seqs);
- int len = 0;
+ setReverseOrder(align, seqs);
+ }
- if ((nSeq % 2) == 0)
- {
- len = nSeq / 2;
- }
- else
- {
- len = (nSeq + 1) / 2;
- }
+ /**
+ * Reverse the order of the sort
+ *
+ * @param align DOCUMENT ME!
+ * @param seqs DOCUMENT ME!
+ */
+ private static void setReverseOrder(AlignmentI align, SequenceI[] seqs)
+ {
+ int nSeq = seqs.length;
- // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
- for (int i = 0; i < len; i++)
- {
- //SequenceI tmp = seqs[i];
- align.getSequences().setElementAt(seqs[nSeq - i - 1], i);
- align.getSequences().setElementAt(seqs[i], nSeq - i - 1);
- }
+ int len = 0;
+
+ if ( (nSeq % 2) == 0)
+ {
+ len = nSeq / 2;
+ }
+ else
+ {
+ len = (nSeq + 1) / 2;
}
- /**
- * Sets the Alignment object with the given sequences
- *
- * @param align Alignment object to be updated
- * @param tmp sequences as a vector
- */
- private static void setOrder(AlignmentI align, Vector tmp)
+ // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
+ for (int i = 0; i < len; i++)
+ {
+ //SequenceI tmp = seqs[i];
+ align.getSequences().setElementAt(seqs[nSeq - i - 1], i);
+ align.getSequences().setElementAt(seqs[i], nSeq - i - 1);
+ }
+ }
+
+ /**
+ * Sets the Alignment object with the given sequences
+ *
+ * @param align Alignment object to be updated
+ * @param tmp sequences as a vector
+ */
+ private static void setOrder(AlignmentI align, Vector tmp)
+ {
+ setOrder(align, vectorSubsetToArray(tmp, align.getSequences()));
+ }
+
+ /**
+ * Sets the Alignment object with the given sequences
+ *
+ * @param align DOCUMENT ME!
+ * @param seqs sequences as an array
+ */
+ public static void setOrder(AlignmentI align, SequenceI[] seqs)
+ {
+ // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
+ Vector algn = align.getSequences();
+ Vector tmp = new Vector();
+
+ for (int i = 0; i < seqs.length; i++)
{
- setOrder(align, vectorSubsetToArray(tmp, align.getSequences()));
+ if (algn.contains(seqs[i]))
+ {
+ tmp.addElement(seqs[i]);
+ }
}
- /**
- * Sets the Alignment object with the given sequences
- *
- * @param align DOCUMENT ME!
- * @param seqs sequences as an array
- */
- public static void setOrder(AlignmentI align, SequenceI[] seqs)
+ algn.removeAllElements();
+ //User may have hidden seqs, then clicked undo or redo
+ for (int i = 0; i < tmp.size(); i++)
{
- // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
- Vector algn = align.getSequences();
- Vector tmp = new Vector();
+ algn.addElement(tmp.elementAt(i));
+ }
- for (int i = 0; i < seqs.length; i++)
- {
- if(algn.contains(seqs[i]))
- tmp.addElement(seqs[i]);
- }
+ }
- algn.removeAllElements();
- //User may have hidden seqs, then clicked undo or redo
- for (int i = 0; i < tmp.size(); i++)
- {
- algn.addElement(tmp.elementAt(i));
- }
+ /**
+ * Sorts by ID. Numbers are sorted before letters.
+ *
+ * @param align The alignment object to sort
+ */
+ public static void sortByID(AlignmentI align)
+ {
+ int nSeq = align.getHeight();
+ String[] ids = new String[nSeq];
+ SequenceI[] seqs = new SequenceI[nSeq];
+ for (int i = 0; i < nSeq; i++)
+ {
+ ids[i] = align.getSequenceAt(i).getName();
+ seqs[i] = align.getSequenceAt(i);
+ }
+ QuickSort.sort(ids, seqs);
+ if (sortIdAscending)
+ {
+ setReverseOrder(align, seqs);
}
-
- /**
- * Sorts by ID. Numbers are sorted before letters.
- *
- * @param align The alignment object to sort
- */
- public static void sortByID(AlignmentI align)
+ else
{
- int nSeq = align.getHeight();
-
- String[] ids = new String[nSeq];
- SequenceI[] seqs = new SequenceI[nSeq];
-
- for (int i = 0; i < nSeq; i++)
- {
- ids[i] = align.getSequenceAt(i).getName();
- seqs[i] = align.getSequenceAt(i);
- }
-
- QuickSort.sort(ids, seqs);
-
- if (sortIdAscending)
- {
- setReverseOrder(align, seqs);
- }
- else
- {
- setOrder(align, seqs);
- }
+ setOrder(align, seqs);
+ }
- sortIdAscending = !sortIdAscending;
+ sortIdAscending = !sortIdAscending;
+ }
+
+ /**
+ * Sorts the alignment by size of group.
+ *
Maintains the order of sequences in each group
+ * by order in given alignment object.
+ *
+ * @param align sorts the given alignment object by group
+ */
+ public static void sortByGroup(AlignmentI align)
+ {
+ //MAINTAINS ORIGNAL SEQUENCE ORDER,
+ //ORDERS BY GROUP SIZE
+ Vector groups = new Vector();
+
+ if (groups.hashCode() != lastGroupHash)
+ {
+ sortGroupAscending = true;
+ lastGroupHash = groups.hashCode();
+ }
+ else
+ {
+ sortGroupAscending = !sortGroupAscending;
}
- /**
- * Sorts the alignment by size of group.
- *
Maintains the order of sequences in each group
- * by order in given alignment object.
- *
- * @param align sorts the given alignment object by group
- */
- public static void sortByGroup(AlignmentI align)
+ //SORTS GROUPS BY SIZE
+ //////////////////////
+ for (int i = 0; i < align.getGroups().size(); i++)
{
- //MAINTAINS ORIGNAL SEQUENCE ORDER,
- //ORDERS BY GROUP SIZE
- Vector groups = new Vector();
+ SequenceGroup sg = (SequenceGroup) align.getGroups().elementAt(i);
- if (groups.hashCode() != lastGroupHash)
- {
- sortGroupAscending = true;
- lastGroupHash = groups.hashCode();
- }
- else
- {
- sortGroupAscending = !sortGroupAscending;
- }
+ for (int j = 0; j < groups.size(); j++)
+ {
+ SequenceGroup sg2 = (SequenceGroup) groups.elementAt(j);
- //SORTS GROUPS BY SIZE
- //////////////////////
- for (int i = 0; i < align.getGroups().size(); i++)
+ if (sg.getSize() > sg2.getSize())
{
- SequenceGroup sg = (SequenceGroup) align.getGroups().elementAt(i);
-
- for (int j = 0; j < groups.size(); j++)
- {
- SequenceGroup sg2 = (SequenceGroup) groups.elementAt(j);
-
- if (sg.getSize() > sg2.getSize())
- {
- groups.insertElementAt(sg, j);
+ groups.insertElementAt(sg, j);
- break;
- }
- }
-
- if (!groups.contains(sg))
- {
- groups.addElement(sg);
- }
+ break;
}
+ }
- //NOW ADD SEQUENCES MAINTAINING ALIGNMENT ORDER
- ///////////////////////////////////////////////
- Vector seqs = new Vector();
+ if (!groups.contains(sg))
+ {
+ groups.addElement(sg);
+ }
+ }
- for (int i = 0; i < groups.size(); i++)
- {
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
- SequenceI[] orderedseqs = sg.getSequencesInOrder(align);
+ //NOW ADD SEQUENCES MAINTAINING ALIGNMENT ORDER
+ ///////////////////////////////////////////////
+ Vector seqs = new Vector();
- for (int j = 0; j < orderedseqs.length; j++)
- {
- seqs.addElement(orderedseqs[j]);
- }
- }
+ for (int i = 0; i < groups.size(); i++)
+ {
+ SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+ SequenceI[] orderedseqs = sg.getSequencesInOrder(align);
- if (sortGroupAscending)
- {
- setOrder(align, seqs);
- }
- else
- {
- setReverseOrder(align,
- vectorSubsetToArray(seqs, align.getSequences()));
- }
+ for (int j = 0; j < orderedseqs.length; j++)
+ {
+ seqs.addElement(orderedseqs[j]);
+ }
}
- /**
- * Converts Vector to array.
- * java 1.18 does not have Vector.toArray()
- *
- * @param tmp Vector of SequenceI objects
- *
- * @return array of Sequence[]
- */
- private static SequenceI[] vectorToArray(Vector tmp)
+ if (sortGroupAscending)
{
- SequenceI[] seqs = new SequenceI[tmp.size()];
-
- for (int i = 0; i < tmp.size(); i++)
- {
- seqs[i] = (SequenceI) tmp.elementAt(i);
- }
-
- return seqs;
+ setOrder(align, seqs);
}
-
- /**
- * DOCUMENT ME!
- *
- * @param tmp DOCUMENT ME!
- * @param mask DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- private static SequenceI[] vectorSubsetToArray(Vector tmp, Vector mask)
+ else
{
- Vector seqs = new Vector();
- int i;
- boolean[] tmask = new boolean[mask.size()];
-
- for (i = 0; i < mask.size(); i++)
- tmask[i] = true;
-
- for (i = 0; i < tmp.size(); i++)
- {
- Object sq = tmp.elementAt(i);
+ setReverseOrder(align,
+ vectorSubsetToArray(seqs, align.getSequences()));
+ }
+ }
+
+ /**
+ * Converts Vector to array.
+ * java 1.18 does not have Vector.toArray()
+ *
+ * @param tmp Vector of SequenceI objects
+ *
+ * @return array of Sequence[]
+ */
+ private static SequenceI[] vectorToArray(Vector tmp)
+ {
+ SequenceI[] seqs = new SequenceI[tmp.size()];
+
+ for (int i = 0; i < tmp.size(); i++)
+ {
+ seqs[i] = (SequenceI) tmp.elementAt(i);
+ }
- if (mask.contains(sq) && tmask[mask.indexOf(sq)])
- {
- tmask[mask.indexOf(sq)] = false;
- seqs.addElement(sq);
- }
- }
+ return seqs;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param tmp DOCUMENT ME!
+ * @param mask DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ private static SequenceI[] vectorSubsetToArray(Vector tmp, Vector mask)
+ {
+ Vector seqs = new Vector();
+ int i;
+ boolean[] tmask = new boolean[mask.size()];
+
+ for (i = 0; i < mask.size(); i++)
+ {
+ tmask[i] = true;
+ }
- for (i = 0; i < tmask.length; i++)
- if (tmask[i])
- {
- seqs.addElement(mask.elementAt(i));
- }
+ for (i = 0; i < tmp.size(); i++)
+ {
+ Object sq = tmp.elementAt(i);
- return vectorToArray(seqs);
+ if (mask.contains(sq) && tmask[mask.indexOf(sq)])
+ {
+ tmask[mask.indexOf(sq)] = false;
+ seqs.addElement(sq);
+ }
}
- /**
- * Sorts by a given AlignmentOrder object
- *
- * @param align Alignment to order
- * @param order specified order for alignment
- */
- public static void sortBy(AlignmentI align, AlignmentOrder order)
+ for (i = 0; i < tmask.length; i++)
{
- // Get an ordered vector of sequences which may also be present in align
- Vector tmp = order.getOrder();
-
- if (lastOrder == order)
- {
- sortOrderAscending = !sortOrderAscending;
- }
- else
- {
- sortOrderAscending = true;
- }
+ if (tmask[i])
+ {
+ seqs.addElement(mask.elementAt(i));
+ }
+ }
- if (sortOrderAscending)
- {
- setOrder(align, tmp);
- }
- else
- {
- setReverseOrder(align,
- vectorSubsetToArray(tmp, align.getSequences()));
- }
+ return vectorToArray(seqs);
+ }
+
+ /**
+ * Sorts by a given AlignmentOrder object
+ *
+ * @param align Alignment to order
+ * @param order specified order for alignment
+ */
+ public static void sortBy(AlignmentI align, AlignmentOrder order)
+ {
+ // Get an ordered vector of sequences which may also be present in align
+ Vector tmp = order.getOrder();
+
+ if (lastOrder == order)
+ {
+ sortOrderAscending = !sortOrderAscending;
+ }
+ else
+ {
+ sortOrderAscending = true;
}
- /**
- * DOCUMENT ME!
- *
- * @param align alignment to order
- * @param tree tree which has
- *
- * @return DOCUMENT ME!
- */
- private static Vector getOrderByTree(AlignmentI align, NJTree tree)
+ if (sortOrderAscending)
{
- int nSeq = align.getHeight();
+ setOrder(align, tmp);
+ }
+ else
+ {
+ setReverseOrder(align,
+ vectorSubsetToArray(tmp, align.getSequences()));
+ }
+ }
- Vector tmp = new Vector();
+ /**
+ * DOCUMENT ME!
+ *
+ * @param align alignment to order
+ * @param tree tree which has
+ *
+ * @return DOCUMENT ME!
+ */
+ private static Vector getOrderByTree(AlignmentI align, NJTree tree)
+ {
+ int nSeq = align.getHeight();
- tmp = _sortByTree(tree.getTopNode(), tmp, align.getSequences());
+ Vector tmp = new Vector();
- if (tmp.size() != nSeq)
- {
- // TODO: JBPNote - decide if this is always an error
- // (eg. not when a tree is associated to another alignment which has more
- // sequences)
- if (tmp.size() < nSeq)
- {
- addStrays(align, tmp);
- }
-
- if (tmp.size() != nSeq)
- {
- System.err.println("ERROR: tmp.size()=" + tmp.size() +
- " != nseq=" + nSeq + " in getOrderByTree");
- }
- }
+ tmp = _sortByTree(tree.getTopNode(), tmp, align.getSequences());
- return tmp;
+ if (tmp.size() != nSeq)
+ {
+ // TODO: JBPNote - decide if this is always an error
+ // (eg. not when a tree is associated to another alignment which has more
+ // sequences)
+ if (tmp.size() < nSeq)
+ {
+ addStrays(align, tmp);
+ }
+
+ if (tmp.size() != nSeq)
+ {
+ System.err.println("ERROR: tmp.size()=" + tmp.size() +
+ " != nseq=" + nSeq + " in getOrderByTree");
+ }
}
- /**
- * Sorts the alignment by a given tree
- *
- * @param align alignment to order
- * @param tree tree which has
- */
- public static void sortByTree(AlignmentI align, NJTree tree)
+ return tmp;
+ }
+
+ /**
+ * Sorts the alignment by a given tree
+ *
+ * @param align alignment to order
+ * @param tree tree which has
+ */
+ public static void sortByTree(AlignmentI align, NJTree tree)
+ {
+ Vector tmp = getOrderByTree(align, tree);
+
+ // tmp should properly permute align with tree.
+ if (lastTree != tree)
{
- Vector tmp = getOrderByTree(align, tree);
-
- // tmp should properly permute align with tree.
- if (lastTree != tree)
- {
- sortTreeAscending = true;
- lastTree = tree;
- }
- else
- {
- sortTreeAscending = !sortTreeAscending;
- }
-
- if (sortTreeAscending)
- {
- setOrder(align, tmp);
- }
- else
- {
- setReverseOrder(align,
- vectorSubsetToArray(tmp, align.getSequences()));
- }
+ sortTreeAscending = true;
+ lastTree = tree;
}
-
- /**
- * DOCUMENT ME!
- *
- * @param align DOCUMENT ME!
- * @param seqs DOCUMENT ME!
- */
- private static void addStrays(AlignmentI align, Vector seqs)
+ else
{
- int nSeq = align.getHeight();
-
- for (int i = 0; i < nSeq; i++)
- {
- if (!seqs.contains(align.getSequenceAt(i)))
- {
- seqs.addElement(align.getSequenceAt(i));
- }
- }
+ sortTreeAscending = !sortTreeAscending;
+ }
- if (nSeq != seqs.size())
- {
- System.err.println(
- "ERROR: Size still not right even after addStrays");
- }
+ if (sortTreeAscending)
+ {
+ setOrder(align, tmp);
+ }
+ else
+ {
+ setReverseOrder(align,
+ vectorSubsetToArray(tmp, align.getSequences()));
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param align DOCUMENT ME!
+ * @param seqs DOCUMENT ME!
+ */
+ private static void addStrays(AlignmentI align, Vector seqs)
+ {
+ int nSeq = align.getHeight();
+
+ for (int i = 0; i < nSeq; i++)
+ {
+ if (!seqs.contains(align.getSequenceAt(i)))
+ {
+ seqs.addElement(align.getSequenceAt(i));
+ }
}
- /**
- * DOCUMENT ME!
- *
- * @param node DOCUMENT ME!
- * @param tmp DOCUMENT ME!
- * @param seqset DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- private static Vector _sortByTree(SequenceNode node, Vector tmp,
- Vector seqset)
+ if (nSeq != seqs.size())
{
- if (node == null)
- {
- return tmp;
- }
+ System.err.println(
+ "ERROR: Size still not right even after addStrays");
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param node DOCUMENT ME!
+ * @param tmp DOCUMENT ME!
+ * @param seqset DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ private static Vector _sortByTree(SequenceNode node, Vector tmp,
+ Vector seqset)
+ {
+ if (node == null)
+ {
+ return tmp;
+ }
- SequenceNode left = (SequenceNode) node.left();
- SequenceNode right = (SequenceNode) node.right();
+ SequenceNode left = (SequenceNode) node.left();
+ SequenceNode right = (SequenceNode) node.right();
- if ((left == null) && (right == null))
- {
- if (!node.isPlaceholder() && (node.element() != null))
- {
- if (node.element() instanceof SequenceI)
- {
- if (!tmp.contains(node.element()))
- {
- tmp.addElement((SequenceI) node.element());
- }
- }
- }
-
- return tmp;
- }
- else
+ if ( (left == null) && (right == null))
+ {
+ if (!node.isPlaceholder() && (node.element() != null))
+ {
+ if (node.element() instanceof SequenceI)
{
- _sortByTree(left, tmp, seqset);
- _sortByTree(right, tmp, seqset);
+ if (!tmp.contains(node.element()))
+ {
+ tmp.addElement( (SequenceI) node.element());
+ }
}
+ }
- return tmp;
+ return tmp;
+ }
+ else
+ {
+ _sortByTree(left, tmp, seqset);
+ _sortByTree(right, tmp, seqset);
}
- // Ordering Objects
- // Alignment.sortBy(OrderObj) - sequence of sequence pointer refs in appropriate order
- //
+ return tmp;
+ }
- /**
- * recover the order of sequences given by the safe numbering scheme introducd
- * SeqsetUtils.uniquify.
- */
- public static void recoverOrder(SequenceI[] alignment)
- {
- float[] ids = new float[alignment.length];
+ // Ordering Objects
+ // Alignment.sortBy(OrderObj) - sequence of sequence pointer refs in appropriate order
+ //
- for (int i = 0; i < alignment.length; i++)
- ids[i] = (new Float(alignment[i].getName().substring(8))).floatValue();
+ /**
+ * recover the order of sequences given by the safe numbering scheme introducd
+ * SeqsetUtils.uniquify.
+ */
+ public static void recoverOrder(SequenceI[] alignment)
+ {
+ float[] ids = new float[alignment.length];
- jalview.util.QuickSort.sort(ids, alignment);
+ for (int i = 0; i < alignment.length; i++)
+ {
+ ids[i] = (new Float(alignment[i].getName().substring(8))).floatValue();
}
+
+ jalview.util.QuickSort.sort(ids, alignment);
+ }
}