-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 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.analysis;\r
-\r
-import jalview.datamodel.*;\r
-\r
-import jalview.util.*;\r
-\r
-import java.util.*;\r
-\r
-\r
-/** Data structure to hold and manipulate a multiple sequence alignment\r
- */\r
-public class AlignmentSorter\r
-{\r
- static boolean sortIdAscending = true;\r
- static int lastGroupHash = 0;\r
- static boolean sortGroupAscending = true;\r
- static AlignmentOrder lastOrder = null;\r
- static boolean sortOrderAscending = true;\r
- static NJTree lastTree = null;\r
- static boolean sortTreeAscending = true;\r
-\r
- /**\r
- * Sort by Percentage Identity\r
- *\r
- * @param align AlignmentI\r
- * @param s SequenceI\r
- */\r
- public static void sortByPID(AlignmentI align, SequenceI s)\r
- {\r
- int nSeq = align.getHeight();\r
-\r
- float[] scores = new float[nSeq];\r
- SequenceI[] seqs = new SequenceI[nSeq];\r
-\r
- for (int i = 0; i < nSeq; i++)\r
- {\r
- scores[i] = Comparison.PID(align.getSequenceAt(i).getSequence(),\r
- s.getSequence());\r
- seqs[i] = align.getSequenceAt(i);\r
- }\r
-\r
- QuickSort.sort(scores, 0, scores.length - 1, seqs);\r
-\r
- setReverseOrder(align, seqs);\r
- }\r
-\r
- /**\r
- * Reverse the order of the sort\r
- *\r
- * @param align DOCUMENT ME!\r
- * @param seqs DOCUMENT ME!\r
- */\r
- private static void setReverseOrder(AlignmentI align, SequenceI[] seqs)\r
- {\r
- int nSeq = seqs.length;\r
-\r
- int len = 0;\r
-\r
- if ((nSeq % 2) == 0)\r
- {\r
- len = nSeq / 2;\r
- }\r
- else\r
- {\r
- len = (nSeq + 1) / 2;\r
- }\r
-\r
- // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work\r
- for (int i = 0; i < len; i++)\r
- {\r
- //SequenceI tmp = seqs[i];\r
- align.getSequences().setElementAt(seqs[nSeq - i - 1], i);\r
- align.getSequences().setElementAt(seqs[i], nSeq - i - 1);\r
- }\r
- }\r
-\r
- /**\r
- * Sets the Alignment object with the given sequences\r
- *\r
- * @param align Alignment object to be updated\r
- * @param tmp sequences as a vector\r
- */\r
- private static void setOrder(AlignmentI align, Vector tmp)\r
- {\r
- setOrder(align, vectorSubsetToArray(tmp, align.getSequences()));\r
- }\r
-\r
- /**\r
- * Sets the Alignment object with the given sequences\r
- *\r
- * @param align DOCUMENT ME!\r
- * @param seqs sequences as an array\r
- */\r
- private static void setOrder(AlignmentI align, SequenceI[] seqs)\r
- {\r
- // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work\r
- Vector algn = align.getSequences();\r
-\r
- for (int i = 0; i < seqs.length; i++)\r
- {\r
- algn.setElementAt(seqs[i], i);\r
- }\r
- }\r
-\r
- /**\r
- * Sorts by ID. Numbers are sorted before letters.\r
- *\r
- * @param align The alignment object to sort\r
- */\r
- public static void sortByID(AlignmentI align)\r
- {\r
- int nSeq = align.getHeight();\r
-\r
- String[] ids = new String[nSeq];\r
- SequenceI[] seqs = new SequenceI[nSeq];\r
-\r
- for (int i = 0; i < nSeq; i++)\r
- {\r
- ids[i] = align.getSequenceAt(i).getName();\r
- seqs[i] = align.getSequenceAt(i);\r
- }\r
-\r
- QuickSort.sort(ids, seqs);\r
-\r
- if (sortIdAscending)\r
- {\r
- setReverseOrder(align, seqs);\r
- }\r
- else\r
- {\r
- setOrder(align, seqs);\r
- }\r
-\r
- sortIdAscending = !sortIdAscending;\r
- }\r
-\r
- /**\r
- * Sorts the alignment by size of group.\r
- * <br>Maintains the order of sequences in each group\r
- * by order in given alignment object.\r
- *\r
- * @param align sorts the given alignment object by group\r
- */\r
- public static void sortByGroup(AlignmentI align)\r
- {\r
- //MAINTAINS ORIGNAL SEQUENCE ORDER,\r
- //ORDERS BY GROUP SIZE\r
- Vector groups = new Vector();\r
-\r
- if (groups.hashCode() != lastGroupHash)\r
- {\r
- sortGroupAscending = true;\r
- lastGroupHash = groups.hashCode();\r
- }\r
- else\r
- {\r
- sortGroupAscending = !sortGroupAscending;\r
- }\r
-\r
- //SORTS GROUPS BY SIZE\r
- //////////////////////\r
- for (int i = 0; i < align.getGroups().size(); i++)\r
- {\r
- SequenceGroup sg = (SequenceGroup) align.getGroups().elementAt(i);\r
-\r
- for (int j = 0; j < groups.size(); j++)\r
- {\r
- SequenceGroup sg2 = (SequenceGroup) groups.elementAt(j);\r
-\r
- if (sg.getSize(false) > sg2.getSize(false))\r
- {\r
- groups.insertElementAt(sg, j);\r
-\r
- break;\r
- }\r
- }\r
-\r
- if (!groups.contains(sg))\r
- {\r
- groups.addElement(sg);\r
- }\r
- }\r
-\r
- //NOW ADD SEQUENCES MAINTAINING ALIGNMENT ORDER\r
- ///////////////////////////////////////////////\r
- Vector seqs = new Vector();\r
-\r
- for (int i = 0; i < groups.size(); i++)\r
- {\r
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
- SequenceI[] orderedseqs = sg.getSequencesInOrder(align);\r
-\r
- for (int j = 0; j < orderedseqs.length; j++)\r
- {\r
- seqs.addElement(orderedseqs[j]);\r
- }\r
- }\r
-\r
- if (sortGroupAscending)\r
- {\r
- setOrder(align, seqs);\r
- }\r
- else\r
- {\r
- setReverseOrder(align,\r
- vectorSubsetToArray(seqs, align.getSequences()));\r
- }\r
- }\r
-\r
- /**\r
- * Converts Vector to array.\r
- * java 1.18 does not have Vector.toArray()\r
- *\r
- * @param tmp Vector of SequenceI objects\r
- *\r
- * @return array of Sequence[]\r
- */\r
- private static SequenceI[] vectorToArray(Vector tmp)\r
- {\r
- SequenceI[] seqs = new SequenceI[tmp.size()];\r
-\r
- for (int i = 0; i < tmp.size(); i++)\r
- {\r
- seqs[i] = (SequenceI) tmp.elementAt(i);\r
- }\r
-\r
- return seqs;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param tmp DOCUMENT ME!\r
- * @param mask DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- private static SequenceI[] vectorSubsetToArray(Vector tmp, Vector mask)\r
- {\r
- Vector seqs = new Vector();\r
- int i;\r
- boolean[] tmask = new boolean[mask.size()];\r
-\r
- for (i = 0; i < mask.size(); i++)\r
- tmask[i] = true;\r
-\r
- for (i = 0; i < tmp.size(); i++)\r
- {\r
- Object sq = tmp.elementAt(i);\r
-\r
- if (mask.contains(sq) && tmask[mask.indexOf(sq)])\r
- {\r
- tmask[mask.indexOf(sq)] = false;\r
- seqs.addElement(sq);\r
- }\r
- }\r
-\r
- for (i = 0; i < tmask.length; i++)\r
- if (tmask[i])\r
- {\r
- seqs.addElement(mask.elementAt(i));\r
- }\r
-\r
- return vectorToArray(seqs);\r
- }\r
-\r
- /**\r
- * Sorts by a given AlignmentOrder object\r
- *\r
- * @param align Alignment to order\r
- * @param order specified order for alignment\r
- */\r
- public static void sortBy(AlignmentI align, AlignmentOrder order)\r
- {\r
- // Get an ordered vector of sequences which may also be present in align\r
- Vector tmp = order.getOrder();\r
-\r
- if (lastOrder == order)\r
- {\r
- sortOrderAscending = !sortOrderAscending;\r
- }\r
- else\r
- {\r
- sortOrderAscending = true;\r
- }\r
-\r
- if (sortOrderAscending)\r
- {\r
- setOrder(align, tmp);\r
- }\r
- else\r
- {\r
- setReverseOrder(align,\r
- vectorSubsetToArray(tmp, align.getSequences()));\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param align alignment to order\r
- * @param tree tree which has\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- private static Vector getOrderByTree(AlignmentI align, NJTree tree)\r
- {\r
- int nSeq = align.getHeight();\r
-\r
- Vector tmp = new Vector();\r
-\r
- tmp = _sortByTree(tree.getTopNode(), tmp, align.getSequences());\r
-\r
- if (tmp.size() != nSeq)\r
- {\r
- // TODO: JBPNote - decide if this is always an error\r
- // (eg. not when a tree is associated to another alignment which has more\r
- // sequences)\r
- if (tmp.size() < nSeq)\r
- {\r
- addStrays(align, tmp);\r
- }\r
-\r
- if (tmp.size() != nSeq)\r
- {\r
- System.err.println("ERROR: tmp.size()=" + tmp.size() +\r
- " != nseq=" + nSeq + " in getOrderByTree");\r
- }\r
- }\r
-\r
- return tmp;\r
- }\r
-\r
- /**\r
- * Sorts the alignment by a given tree\r
- *\r
- * @param align alignment to order\r
- * @param tree tree which has\r
- */\r
- public static void sortByTree(AlignmentI align, NJTree tree)\r
- {\r
- Vector tmp = getOrderByTree(align, tree);\r
-\r
- // tmp should properly permute align with tree.\r
- if (lastTree != tree)\r
- {\r
- sortTreeAscending = true;\r
- lastTree = tree;\r
- }\r
- else\r
- {\r
- sortTreeAscending = !sortTreeAscending;\r
- }\r
-\r
- if (sortTreeAscending)\r
- {\r
- setOrder(align, tmp);\r
- }\r
- else\r
- {\r
- setReverseOrder(align,\r
- vectorSubsetToArray(tmp, align.getSequences()));\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param align DOCUMENT ME!\r
- * @param seqs DOCUMENT ME!\r
- */\r
- private static void addStrays(AlignmentI align, Vector seqs)\r
- {\r
- int nSeq = align.getHeight();\r
-\r
- for (int i = 0; i < nSeq; i++)\r
- {\r
- if (!seqs.contains(align.getSequenceAt(i)))\r
- {\r
- seqs.addElement(align.getSequenceAt(i));\r
- }\r
- }\r
-\r
- if (nSeq != seqs.size())\r
- {\r
- System.err.println(\r
- "ERROR: Size still not right even after addStrays");\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param node DOCUMENT ME!\r
- * @param tmp DOCUMENT ME!\r
- * @param seqset DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- private static Vector _sortByTree(SequenceNode node, Vector tmp,\r
- Vector seqset)\r
- {\r
- if (node == null)\r
- {\r
- return tmp;\r
- }\r
-\r
- SequenceNode left = (SequenceNode) node.left();\r
- SequenceNode right = (SequenceNode) node.right();\r
-\r
- if ((left == null) && (right == null))\r
- {\r
- if (!node.isPlaceholder() && (node.element() != null))\r
- {\r
- if (node.element() instanceof SequenceI)\r
- {\r
- if (!tmp.contains(node.element()))\r
- {\r
- tmp.addElement((SequenceI) node.element());\r
- }\r
- }\r
- }\r
-\r
- return tmp;\r
- }\r
- else\r
- {\r
- _sortByTree(left, tmp, seqset);\r
- _sortByTree(right, tmp, seqset);\r
- }\r
-\r
- return tmp;\r
- }\r
-\r
- // Ordering Objects\r
- // Alignment.sortBy(OrderObj) - sequence of sequence pointer refs in appropriate order\r
- //\r
-\r
- /**\r
- * recover the order of sequences given by the safe numbering scheme introducd\r
- * SeqsetUtils.uniquify.\r
- */\r
- public static void recoverOrder(SequenceI[] alignment)\r
- {\r
- float[] ids = new float[alignment.length];\r
-\r
- for (int i = 0; i < alignment.length; i++)\r
- ids[i] = (new Float(alignment[i].getName().substring(8))).floatValue();\r
-\r
- jalview.util.QuickSort.sort(ids, alignment);\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.analysis;
+
+import jalview.analysis.scoremodels.PIDModel;
+import jalview.analysis.scoremodels.SimilarityParams;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentOrder;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequenceNode;
+import jalview.ext.treeviewer.TreeI;
+import jalview.ext.treeviewer.TreeNodeI;
+import jalview.util.QuickSort;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
+/**
+ * Routines for manipulating the order of a multiple sequence alignment TODO:
+ * this class retains some global states concerning sort-order which should be
+ * made attributes for the caller's alignment visualization. TODO: refactor to
+ * allow a subset of selected sequences to be sorted within the context of a
+ * whole alignment. Sort method template is: SequenceI[] tobesorted, [ input
+ * data mapping to each tobesorted element to use ], Alignment context of
+ * tobesorted that are to be re-ordered, boolean sortinplace, [special data - ie
+ * seuqence to be sorted w.r.t.]) sortinplace implies that the sorted vector
+ * resulting from applying the operation to tobesorted should be mapped back to
+ * the original positions in alignment. Otherwise, normal behaviour is to re
+ * order alignment so that tobesorted is sorted and grouped together starting
+ * from the first tobesorted position in the alignment. e.g. (a,tb2,b,tb1,c,tb3
+ * becomes a,tb1,tb2,tb3,b,c)
+ */
+public class AlignmentSorter
+{
+ /*
+ * todo: refactor searches to follow a basic pattern: (search property, last
+ * search state, current sort direction)
+ */
+ static boolean sortIdAscending = true;
+
+ static int lastGroupHash = 0;
+
+ static boolean sortGroupAscending = true;
+
+ static AlignmentOrder lastOrder = null;
+
+ static boolean sortOrderAscending = true;
+
+ static TreeModel lastTree = null;
+
+ static TreeI lastExternalTree = null;
+
+ static boolean sortTreeAscending = true;
+
+ /*
+ * last Annotation Label used for sort by Annotation score
+ */
+ private static String lastSortByAnnotation;
+
+ /*
+ * string hash of last arguments to sortByFeature
+ * (sort order toggles if this is unchanged between sorts)
+ */
+ private static String sortByFeatureCriteria;
+
+ private static boolean sortByFeatureAscending = true;
+
+ private static boolean sortLengthAscending;
+
+ /**
+ * Sorts sequences in the alignment by Percentage Identity with the given
+ * reference sequence, sorting the highest identity to the top
+ *
+ * @param align
+ * AlignmentI
+ * @param s
+ * SequenceI
+ * @param end
+ */
+ public static void sortByPID(AlignmentI align, SequenceI s)
+ {
+ int nSeq = align.getHeight();
+
+ float[] scores = new float[nSeq];
+ SequenceI[] seqs = new SequenceI[nSeq];
+ String refSeq = s.getSequenceAsString();
+
+ SimilarityParams pidParams = new SimilarityParams(true, true, true,
+ true);
+ for (int i = 0; i < nSeq; i++)
+ {
+ scores[i] = (float) PIDModel.computePID(
+ align.getSequenceAt(i).getSequenceAsString(), refSeq,
+ pidParams);
+ seqs[i] = align.getSequenceAt(i);
+ }
+
+ QuickSort.sort(scores, seqs);
+
+ setReverseOrder(align, seqs);
+ }
+
+ /**
+ * 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
+ List<SequenceI> asq = align.getSequences();
+ synchronized (asq)
+ {
+ for (int i = 0; i < len; i++)
+ {
+ // SequenceI tmp = seqs[i];
+ asq.set(i, seqs[nSeq - i - 1]);
+ asq.set(nSeq - i - 1, seqs[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, List<SequenceI> 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
+ List<SequenceI> algn = align.getSequences();
+ synchronized (algn)
+ {
+ List<SequenceI> tmp = new ArrayList<>();
+
+ for (int i = 0; i < seqs.length; i++)
+ {
+ if (algn.contains(seqs[i]))
+ {
+ tmp.add(seqs[i]);
+ }
+ }
+
+ algn.clear();
+ // User may have hidden seqs, then clicked undo or redo
+ for (int i = 0; i < tmp.size(); i++)
+ {
+ algn.add(tmp.get(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);
+ }
+ else
+ {
+ setOrder(align, seqs);
+ }
+
+ sortIdAscending = !sortIdAscending;
+ }
+
+ /**
+ * Sorts by sequence length
+ *
+ * @param align
+ * The alignment object to sort
+ */
+ public static void sortByLength(AlignmentI align)
+ {
+ int nSeq = align.getHeight();
+
+ float[] length = new float[nSeq];
+ SequenceI[] seqs = new SequenceI[nSeq];
+
+ for (int i = 0; i < nSeq; i++)
+ {
+ seqs[i] = align.getSequenceAt(i);
+ length[i] = (seqs[i].getEnd() - seqs[i].getStart());
+ }
+
+ QuickSort.sort(length, seqs);
+
+ if (sortLengthAscending)
+ {
+ setReverseOrder(align, seqs);
+ }
+ else
+ {
+ setOrder(align, seqs);
+ }
+
+ sortLengthAscending = !sortLengthAscending;
+ }
+
+ /**
+ * Sorts the alignment by size of group. <br>
+ * 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
+ List<SequenceGroup> groups = new ArrayList<>();
+
+ if (groups.hashCode() != lastGroupHash)
+ {
+ sortGroupAscending = true;
+ lastGroupHash = groups.hashCode();
+ }
+ else
+ {
+ sortGroupAscending = !sortGroupAscending;
+ }
+
+ // SORTS GROUPS BY SIZE
+ // ////////////////////
+ for (SequenceGroup sg : align.getGroups())
+ {
+ for (int j = 0; j < groups.size(); j++)
+ {
+ SequenceGroup sg2 = groups.get(j);
+
+ if (sg.getSize() > sg2.getSize())
+ {
+ groups.add(j, sg);
+
+ break;
+ }
+ }
+
+ if (!groups.contains(sg))
+ {
+ groups.add(sg);
+ }
+ }
+
+ // NOW ADD SEQUENCES MAINTAINING ALIGNMENT ORDER
+ // /////////////////////////////////////////////
+ List<SequenceI> seqs = new ArrayList<>();
+
+ for (int i = 0; i < groups.size(); i++)
+ {
+ SequenceGroup sg = groups.get(i);
+ SequenceI[] orderedseqs = sg.getSequencesInOrder(align);
+
+ for (int j = 0; j < orderedseqs.length; j++)
+ {
+ seqs.add(orderedseqs[j]);
+ }
+ }
+
+ if (sortGroupAscending)
+ {
+ setOrder(align, seqs);
+ }
+ else
+ {
+ setReverseOrder(align,
+ vectorSubsetToArray(seqs, align.getSequences()));
+ }
+ }
+
+ /**
+ * Select sequences in order from tmp that is present in mask, and any
+ * remaining sequences in mask not in tmp
+ *
+ * @param tmp
+ * thread safe collection of sequences
+ * @param mask
+ * thread safe collection of sequences
+ *
+ * @return intersect(tmp,mask)+intersect(complement(tmp),mask)
+ */
+ private static SequenceI[] vectorSubsetToArray(List<SequenceI> tmp,
+ List<SequenceI> mask)
+ {
+ // or?
+ // tmp2 = tmp.retainAll(mask);
+ // return tmp2.addAll(mask.removeAll(tmp2))
+
+ ArrayList<SequenceI> seqs = new ArrayList<>();
+ int i, idx;
+ boolean[] tmask = new boolean[mask.size()];
+
+ for (i = 0; i < mask.size(); i++)
+ {
+ tmask[i] = true;
+ }
+
+ for (i = 0; i < tmp.size(); i++)
+ {
+ SequenceI sq = tmp.get(i);
+ idx = mask.indexOf(sq);
+ if (idx > -1 && tmask[idx])
+ {
+ tmask[idx] = false;
+ seqs.add(sq);
+ }
+ }
+
+ for (i = 0; i < tmask.length; i++)
+ {
+ if (tmask[i])
+ {
+ seqs.add(mask.get(i));
+ }
+ }
+
+ return seqs.toArray(new SequenceI[seqs.size()]);
+ }
+
+ /**
+ * 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
+ List<SequenceI> tmp = order.getOrder();
+
+ if (lastOrder == order)
+ {
+ sortOrderAscending = !sortOrderAscending;
+ }
+ else
+ {
+ sortOrderAscending = true;
+ }
+
+ if (sortOrderAscending)
+ {
+ setOrder(align, tmp);
+ }
+ else
+ {
+ setReverseOrder(align,
+ vectorSubsetToArray(tmp, align.getSequences()));
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param align
+ * alignment to order
+ * @param tree
+ * tree which has
+ *
+ * @return DOCUMENT ME!
+ */
+ private static List<SequenceI> getOrderByTree(AlignmentI align,
+ TreeModel tree)
+ {
+ int nSeq = align.getHeight();
+
+ List<SequenceI> tmp = new ArrayList<>();
+
+ tmp = _sortByTree(tree.getTopNode(), 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("WARNING: tmp.size()=" + tmp.size() + " != nseq="
+ + nSeq
+ + " in getOrderByTree - tree contains sequences not in alignment");
+ }
+ }
+
+ return tmp;
+ }
+
+
+
+ private static List<SequenceI> getOrderByTree(TreeI aptxTree,
+ Map<TreeNodeI, SequenceI> nodesWithBoundSeqs)
+ {
+ List<SequenceI> seqsByTreeOrder = new ArrayList<>();
+ if (!aptxTree.isEmpty())
+ {
+ for (final Iterator<TreeNodeI> iter = aptxTree
+ .iterateInPreOrder(); iter.hasNext();)
+ {
+ TreeNodeI treeNode = iter.next();
+ seqsByTreeOrder.add(nodesWithBoundSeqs.get(treeNode));
+ }
+
+ }
+ return seqsByTreeOrder;
+
+
+ }
+
+ /**
+ * Sorts the alignment by a given tree
+ *
+ * @param align
+ * alignment to order
+ * @param tree
+ * tree which has
+ */
+ public static void sortByTree(AlignmentI align, TreeModel tree)
+ {
+ List<SequenceI> 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()));
+ }
+ }
+
+ /**
+ * Sorts the alignment by a given tree from Archaeopteryx
+ *
+ * @param align
+ * alignment to order
+ * @param tree
+ * tree which has
+ */
+ public static void sortByTree(AlignmentI align,
+ Map<TreeNodeI, SequenceI> nodesBoundToSequences,
+ TreeI treeI) throws IllegalArgumentException
+ {
+ List<SequenceI> tmp = getOrderByTree(treeI, nodesBoundToSequences);
+
+ if (!tmp.isEmpty())
+ {
+ if (lastExternalTree != treeI)
+ {
+ sortTreeAscending = true;
+ lastExternalTree = treeI;
+ }
+ else
+ {
+ sortTreeAscending = !sortTreeAscending;
+ }
+
+ if (sortTreeAscending)
+ {
+ setOrder(align, tmp);
+ }
+ else
+ {
+ setReverseOrder(align,
+ vectorSubsetToArray(tmp, align.getSequences()));
+ }
+ }
+ else
+ {
+ throw new IllegalArgumentException();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param align
+ * DOCUMENT ME!
+ * @param tmp
+ * DOCUMENT ME!
+ */
+ private static void addStrays(AlignmentI align, List<SequenceI> tmp)
+ {
+ int nSeq = align.getHeight();
+
+ for (int i = 0; i < nSeq; i++)
+ {
+ if (!tmp.contains(align.getSequenceAt(i)))
+ {
+ tmp.add(align.getSequenceAt(i));
+ }
+ }
+
+ if (nSeq != tmp.size())
+ {
+ 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 List<SequenceI> _sortByTree(SequenceNode node,
+ List<SequenceI> tmp)
+ {
+ 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())) // && (seqset==null ||
+ // seqset.size()==0 ||
+ // seqset.contains(tmp)))
+ {
+ tmp.add((SequenceI) node.element());
+ }
+ }
+ }
+
+ return tmp;
+ }
+ else
+ {
+ _sortByTree(left, tmp);
+ _sortByTree(right, tmp);
+ }
+
+ return tmp;
+ }
+
+
+
+ // Ordering Objects
+ // Alignment.sortBy(OrderObj) - sequence of sequence pointer refs in
+ // appropriate order
+ //
+
+ /**
+ * 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];
+
+ for (int i = 0; i < alignment.length; i++)
+ {
+ ids[i] = (Float.valueOf(alignment[i].getName().substring(8)))
+ .floatValue();
+ }
+
+ jalview.util.QuickSort.sort(ids, alignment);
+ }
+
+ /**
+ * Sort sequence in order of increasing score attribute for annotation with a
+ * particular scoreLabel. Or reverse if same label was used previously
+ *
+ * @param scoreLabel
+ * exact label for sequence associated AlignmentAnnotation scores to
+ * use for sorting.
+ * @param alignment
+ * sequences to be sorted
+ */
+ public static void sortByAnnotationScore(String scoreLabel,
+ AlignmentI alignment)
+ {
+ SequenceI[] seqs = alignment.getSequencesArray();
+ boolean[] hasScore = new boolean[seqs.length]; // per sequence score
+ // presence
+ int hasScores = 0; // number of scores present on set
+ double[] scores = new double[seqs.length];
+ double min = 0, max = 0;
+ for (int i = 0; i < seqs.length; i++)
+ {
+ AlignmentAnnotation[] scoreAnn = seqs[i].getAnnotation(scoreLabel);
+ if (scoreAnn != null)
+ {
+ hasScores++;
+ hasScore[i] = true;
+ scores[i] = scoreAnn[0].getScore(); // take the first instance of this
+ // score.
+ if (hasScores == 1)
+ {
+ max = min = scores[i];
+ }
+ else
+ {
+ if (max < scores[i])
+ {
+ max = scores[i];
+ }
+ if (min > scores[i])
+ {
+ min = scores[i];
+ }
+ }
+ }
+ else
+ {
+ hasScore[i] = false;
+ }
+ }
+ if (hasScores == 0)
+ {
+ return; // do nothing - no scores present to sort by.
+ }
+ if (hasScores < seqs.length)
+ {
+ for (int i = 0; i < seqs.length; i++)
+ {
+ if (!hasScore[i])
+ {
+ scores[i] = (max + i + 1.0);
+ }
+ }
+ }
+
+ jalview.util.QuickSort.sort(scores, seqs);
+ if (lastSortByAnnotation != scoreLabel)
+ {
+ lastSortByAnnotation = scoreLabel;
+ setOrder(alignment, seqs);
+ }
+ else
+ {
+ setReverseOrder(alignment, seqs);
+ }
+ }
+
+ /**
+ * types of feature ordering: Sort by score : average score - or total score -
+ * over all features in region Sort by feature label text: (or if null -
+ * feature type text) - numerical or alphabetical Sort by feature density:
+ * based on counts - ignoring individual text or scores for each feature
+ */
+ public static String FEATURE_SCORE = "average_score";
+
+ public static String FEATURE_LABEL = "text";
+
+ public static String FEATURE_DENSITY = "density";
+
+ /**
+ * Sort sequences by feature score or density, optionally restricted by
+ * feature types, feature groups, or alignment start/end positions.
+ * <p>
+ * If the sort is repeated for the same combination of types and groups, sort
+ * order is reversed.
+ *
+ * @param featureTypes
+ * a list of feature types to include (or null for all)
+ * @param groups
+ * a list of feature groups to include (or null for all)
+ * @param startCol
+ * start column position to include (base zero)
+ * @param endCol
+ * end column position to include (base zero)
+ * @param alignment
+ * the alignment to be sorted
+ * @param method
+ * either "average_score" or "density" ("text" not yet implemented)
+ */
+ public static void sortByFeature(List<String> featureTypes,
+ List<String> groups, final int startCol, final int endCol,
+ AlignmentI alignment, String method)
+ {
+ if (method != FEATURE_SCORE && method != FEATURE_LABEL
+ && method != FEATURE_DENSITY)
+ {
+ String msg = String.format(
+ "Implementation Error - sortByFeature method must be either '%s' or '%s'",
+ FEATURE_SCORE, FEATURE_DENSITY);
+ System.err.println(msg);
+ return;
+ }
+
+ flipFeatureSortIfUnchanged(method, featureTypes, groups, startCol,
+ endCol);
+
+ SequenceI[] seqs = alignment.getSequencesArray();
+
+ boolean[] hasScore = new boolean[seqs.length]; // per sequence score
+ // presence
+ int hasScores = 0; // number of scores present on set
+ double[] scores = new double[seqs.length];
+ int[] seqScores = new int[seqs.length];
+ Object[][] feats = new Object[seqs.length][];
+ double min = 0d;
+ double max = 0d;
+
+ for (int i = 0; i < seqs.length; i++)
+ {
+ /*
+ * get sequence residues overlapping column region
+ * and features for residue positions and specified types
+ */
+ String[] types = featureTypes == null ? null
+ : featureTypes.toArray(new String[featureTypes.size()]);
+ List<SequenceFeature> sfs = seqs[i].findFeatures(startCol + 1,
+ endCol + 1, types);
+
+ seqScores[i] = 0;
+ scores[i] = 0.0;
+
+ Iterator<SequenceFeature> it = sfs.listIterator();
+ while (it.hasNext())
+ {
+ SequenceFeature sf = it.next();
+
+ /*
+ * accept all features with null or empty group, otherwise
+ * check group is one of the currently visible groups
+ */
+ String featureGroup = sf.getFeatureGroup();
+ if (groups != null && featureGroup != null
+ && !"".equals(featureGroup)
+ && !groups.contains(featureGroup))
+ {
+ it.remove();
+ }
+ else
+ {
+ float score = sf.getScore();
+ if (FEATURE_SCORE.equals(method) && !Float.isNaN(score))
+ {
+ if (seqScores[i] == 0)
+ {
+ hasScores++;
+ }
+ seqScores[i]++;
+ hasScore[i] = true;
+ scores[i] += score;
+ // take the first instance of this score // ??
+ }
+ }
+ }
+
+ feats[i] = sfs.toArray(new SequenceFeature[sfs.size()]);
+ if (!sfs.isEmpty())
+ {
+ if (method == FEATURE_LABEL)
+ {
+ // order the labels by alphabet (not yet implemented)
+ String[] labs = new String[sfs.size()];
+ for (int l = 0; l < sfs.size(); l++)
+ {
+ SequenceFeature sf = sfs.get(l);
+ String description = sf.getDescription();
+ labs[l] = (description != null ? description : sf.getType());
+ }
+ QuickSort.sort(labs, feats[i]);
+ }
+ }
+ if (hasScore[i])
+ {
+ // compute average score
+ scores[i] /= seqScores[i];
+ // update the score bounds.
+ if (hasScores == 1)
+ {
+ min = scores[i];
+ max = min;
+ }
+ else
+ {
+ max = Math.max(max, scores[i]);
+ min = Math.min(min, scores[i]);
+ }
+ }
+ }
+
+ if (FEATURE_SCORE.equals(method))
+ {
+ if (hasScores == 0)
+ {
+ return; // do nothing - no scores present to sort by.
+ }
+ // pad score matrix
+ if (hasScores < seqs.length)
+ {
+ for (int i = 0; i < seqs.length; i++)
+ {
+ if (!hasScore[i])
+ {
+ scores[i] = (max + 1 + i);
+ }
+ else
+ {
+ // int nf = (feats[i] == null) ? 0
+ // : ((SequenceFeature[]) feats[i]).length;
+ // // System.err.println("Sorting on Score: seq " +
+ // seqs[i].getName()
+ // + " Feats: " + nf + " Score : " + scores[i]);
+ }
+ }
+ }
+ QuickSort.sortByDouble(scores, seqs, sortByFeatureAscending);
+ }
+ else if (FEATURE_DENSITY.equals(method))
+ {
+ for (int i = 0; i < seqs.length; i++)
+ {
+ int featureCount = feats[i] == null ? 0
+ : ((SequenceFeature[]) feats[i]).length;
+ scores[i] = featureCount;
+ // System.err.println("Sorting on Density: seq "+seqs[i].getName()+
+ // " Feats: "+featureCount+" Score : "+scores[i]);
+ }
+ QuickSort.sortByDouble(scores, seqs, sortByFeatureAscending);
+ }
+
+ setOrder(alignment, seqs);
+ }
+
+ /**
+ * Builds a string hash of criteria for sorting, and if unchanged from last
+ * time, reverse the sort order
+ *
+ * @param method
+ * @param featureTypes
+ * @param groups
+ * @param startCol
+ * @param endCol
+ */
+ protected static void flipFeatureSortIfUnchanged(String method,
+ List<String> featureTypes, List<String> groups,
+ final int startCol, final int endCol)
+ {
+ StringBuilder sb = new StringBuilder(64);
+ sb.append(startCol).append(method).append(endCol);
+ if (featureTypes != null)
+ {
+ Collections.sort(featureTypes);
+ sb.append(featureTypes.toString());
+ }
+ if (groups != null)
+ {
+ Collections.sort(groups);
+ sb.append(groups.toString());
+ }
+ String scoreCriteria = sb.toString();
+
+ /*
+ * if resorting on the same criteria, toggle sort order
+ */
+ if (sortByFeatureCriteria == null
+ || !scoreCriteria.equals(sortByFeatureCriteria))
+ {
+ sortByFeatureAscending = true;
+ }
+ else
+ {
+ sortByFeatureAscending = !sortByFeatureAscending;
+ }
+ sortByFeatureCriteria = scoreCriteria;
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff