X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=20101dc908c91448b86c396dc648548c6024b45c;hb=4f01ddc72d2297c48c57d4f9c25af45b300df154;hp=64682c1f2433e0f2ba9fec3587dee3e5b9eaccd9;hpb=263b70c6c296776e942b7875023cafd293dee0b4;p=jalview.git
diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 64682c1..20101dc 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -1,199 +1,469 @@
+/*
+* 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.analysis;
import jalview.datamodel.*;
+
import jalview.util.*;
-import jalview.io.*;
import java.util.*;
+
/** Data structure to hold and manipulate a multiple sequence alignment
*/
-public class AlignmentSorter {
-
- private AlignmentSorter() {
- }
-
- public static void sortGroups(AlignmentI align) {
- Vector groups = align.getGroups();
- int nGroup = groups.size();
-
- float[] arr = new float [nGroup];
- Object[] s = new Object[nGroup];
-
- for (int i=0; i < nGroup; i++) {
- arr[i] = ((SequenceGroup)groups.elementAt(i)).getSize();
- s[i] = groups.elementAt(i);
+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), s);
+ seqs[i] = align.getSequenceAt(i);
+ }
+
+ QuickSort.sort(scores, 0, scores.length - 1, seqs);
+
+ setReverseOrder(align, seqs);
}
- QuickSort.sort(arr,s);
-
- Vector newg = new Vector(nGroup);
-
- for (int i=nGroup-1; i >= 0; i--) {
- newg.addElement(s[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;
+
+ int len = 0;
+
+ if ((nSeq % 2) == 0)
+ {
+ len = nSeq / 2;
+ }
+ else
+ {
+ len = (nSeq + 1) / 2;
+ }
+
+ // 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);
+ }
}
- // align.setGroups(newg);
- }
-
- /** */
- 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.compare(align.getSequenceAt(i),s);
- seqs[i] = align.getSequenceAt(i);
+ /**
+ * 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()));
}
- QuickSort.sort(scores,0,scores.length-1,seqs);
-
- setReverseOrder(align,seqs);
- }
-
- private static void setReverseOrder(AlignmentI align, SequenceI [] seqs) {
- int nSeq = seqs.length;
-
- 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 DOCUMENT ME!
+ * @param seqs sequences as an array
+ */
+ private static void setOrder(AlignmentI align, SequenceI[] seqs)
+ {
+ // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
+ Vector algn = align.getSequences();
+
+ for (int i = 0; i < seqs.length; i++)
+ {
+ algn.setElementAt(seqs[i], i);
+ }
}
-// 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);
+ /**
+ * 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);
+ }
+ else
+ {
+ setOrder(align, seqs);
+ }
+
+ sortIdAscending = !sortIdAscending;
}
- }
-
- private static void setOrder(AlignmentI align, Vector tmp) {
- setOrder(align,vectorToArray(tmp));
- }
- private static void setOrder(AlignmentI align, SequenceI [] seqs) {
-// NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
- for (int i = 0; i < seqs.length; i++) {
- align.getSequences().setElementAt(seqs[i],i);
+ /**
+ * 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 GROUPS BY SIZE
+ //////////////////////
+ for (int i = 0; i < align.getGroups().size(); i++)
+ {
+ 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);
+
+ break;
+ }
+ }
+
+ if (!groups.contains(sg))
+ {
+ groups.addElement(sg);
+ }
+ }
+
+ //NOW ADD SEQUENCES MAINTAINING ALIGNMENT ORDER
+ ///////////////////////////////////////////////
+ Vector seqs = new Vector();
+
+ for (int i = 0; i < groups.size(); i++)
+ {
+ SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+ SequenceI[] orderedseqs = sg.getSequencesInOrder(align);
+
+ for (int j = 0; j < orderedseqs.length; j++)
+ {
+ seqs.addElement(orderedseqs[j]);
+ }
+ }
+
+ if (sortGroupAscending)
+ {
+ setOrder(align, seqs);
+ }
+ else
+ {
+ setReverseOrder(align,
+ vectorSubsetToArray(seqs, align.getSequences()));
+ }
}
- }
-
- /** */
- static boolean sortIdAscending = true;
- 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);
+ /**
+ * 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);
+ }
+
+ return seqs;
}
- QuickSort.sort(ids,seqs);
-
- if(sortIdAscending)
- setReverseOrder(align,seqs);
- else
- setOrder(align, seqs);
-
- sortIdAscending = !sortIdAscending;
- }
-
- static boolean sortGroupAscending = true;
- public static void sortByGroup(AlignmentI align) {
- int nSeq = align.getHeight();
- Vector groups = align.getGroups();
-
- Vector seqs = new Vector();
-
- for (int i=0; i < groups.size(); i++) {
- SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
-
- for (int j = 0; j < sg.getSize(); j++) {
- seqs.addElement(sg.getSequenceAt(j));
- }
+ /**
+ * 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 < tmp.size(); i++)
+ {
+ Object sq = tmp.elementAt(i);
+
+ if (mask.contains(sq) && tmask[mask.indexOf(sq)])
+ {
+ tmask[mask.indexOf(sq)] = false;
+ seqs.addElement(sq);
+ }
+ }
+
+ for (i = 0; i < tmask.length; i++)
+ if (tmask[i])
+ {
+ seqs.addElement(mask.elementAt(i));
+ }
+
+ return vectorToArray(seqs);
}
- if (seqs.size() != nSeq) {
- System.err.println("ERROR: tmp.size() != nseq in sortByGroups");
- if (seqs.size() < nSeq) {
- addStrays(align,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;
+ }
+
+ if (sortOrderAscending)
+ {
+ setOrder(align, tmp);
+ }
+ else
+ {
+ setReverseOrder(align,
+ vectorSubsetToArray(tmp, align.getSequences()));
+ }
}
- if(sortGroupAscending)
- setOrder(align,seqs);
- else
- setReverseOrder( align, vectorToArray(seqs));
-
- sortGroupAscending = ! sortGroupAscending;
- }
+ /**
+ * 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();
+
+ Vector tmp = new Vector();
+
+ tmp = _sortByTree(tree.getTopNode(), tmp, align.getSequences());
+
+ 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");
+ }
+ }
- 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);
+ return tmp;
}
- return seqs;
- }
- static boolean sortTreeAscending = true;
- public static void sortByTree(AlignmentI align, NJTree tree) {
- int nSeq = align.getHeight();
-
- Vector tmp = new Vector();
-
- tmp = _sortByTree(tree.getTopNode(),tmp);
-
- if (tmp.size() != nSeq) {
- System.err.println("ERROR: tmp.size() != nseq in sortByTree");
- if (tmp.size() < nSeq) {
- addStrays(align,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)
+ {
+ sortTreeAscending = true;
+ lastTree = tree;
+ }
+ else
+ {
+ sortTreeAscending = !sortTreeAscending;
+ }
+
+ if (sortTreeAscending)
+ {
+ setOrder(align, tmp);
+ }
+ else
+ {
+ setReverseOrder(align,
+ vectorSubsetToArray(tmp, align.getSequences()));
+ }
}
- if(sortTreeAscending)
- setOrder(align,tmp);
- else
- setReverseOrder(align, vectorToArray(tmp));
+ /**
+ * 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));
+ }
+ }
+
+ if (nSeq != seqs.size())
+ {
+ System.err.println(
+ "ERROR: Size still not right even after addStrays");
+ }
+ }
- sortTreeAscending = !sortTreeAscending;
- }
+ /**
+ * 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();
+
+ 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
+ {
+ _sortByTree(left, tmp, seqset);
+ _sortByTree(right, tmp, seqset);
+ }
- private static void addStrays(AlignmentI align, Vector seqs) {
- int nSeq = align.getHeight();
- for (int i=0;i