-package jalview.analysis;\r
-\r
-import jalview.datamodel.*;\r
-import jalview.util.*;\r
-import jalview.io.*;\r
-\r
-import java.util.*;\r
-\r
-/** Data structure to hold and manipulate a multiple sequence alignment\r
- */\r
-public class AlignmentSorter {\r
-\r
- private AlignmentSorter() {\r
- }\r
-\r
- public static void sortGroups(AlignmentI align) {\r
- Vector groups = align.getGroups();\r
- int nGroup = groups.size();\r
-\r
- float[] arr = new float [nGroup];\r
- Object[] s = new Object[nGroup];\r
-\r
- for (int i=0; i < nGroup; i++) {\r
- arr[i] = ((SequenceGroup)groups.elementAt(i)).getSize();\r
- s[i] = groups.elementAt(i);\r
- }\r
-\r
- QuickSort.sort(arr,s);\r
-\r
- Vector newg = new Vector(nGroup);\r
-\r
- for (int i=nGroup-1; i >= 0; i--) {\r
- newg.addElement(s[i]);\r
- }\r
-\r
- // align.setGroups(newg);\r
- }\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
- 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
- scores[i] = Comparison.compare(align.getSequenceAt(i),s);\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
- private static void setReverseOrder(AlignmentI align, SequenceI [] seqs) {\r
- int nSeq = seqs.length;\r
-\r
- int len = 0;\r
- if (nSeq%2 == 0) {\r
- len = nSeq/2;\r
- } else {\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
- //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
- private static void setOrder(AlignmentI align, Vector tmp) {\r
- setOrder(align,vectorSubsetToArray(tmp, align.getSequences()));\r
- }\r
-\r
- private static void setOrder(AlignmentI align, SequenceI [] seqs) {\r
- // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work\r
-\r
- Vector algn = align.getSequences();\r
-\r
- for (int i = 0, p = 0; i < seqs.length; i++)\r
- algn.setElementAt(seqs[i], p++);\r
- }\r
- /** */\r
- static boolean sortIdAscending = true;\r
- public static void sortByID(AlignmentI align) {\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
- ids[i] = align.getSequenceAt(i).getName();\r
- seqs[i] = align.getSequenceAt(i);\r
- }\r
-\r
- QuickSort.sort(ids,seqs);\r
-\r
- if(sortIdAscending)\r
- setReverseOrder(align,seqs);\r
- else\r
- setOrder(align, seqs);\r
-\r
- sortIdAscending = !sortIdAscending;\r
- }\r
-\r
- static boolean sortGroupAscending = true;\r
- public static void sortByGroup(AlignmentI align) {\r
- int nSeq = align.getHeight();\r
- Vector groups = align.getGroups();\r
-\r
- Vector seqs = new Vector();\r
-\r
- for (int i=0; i < groups.size(); i++) {\r
- SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
-\r
- for (int j = 0; j < sg.getSize(); j++) {\r
- seqs.addElement(sg.getSequenceAt(j));\r
- }\r
- }\r
-\r
- if (seqs.size() != nSeq) {\r
- System.err.println("ERROR: tmp.size() != nseq in sortByGroups");\r
- if (seqs.size() < nSeq) {\r
- addStrays(align,seqs);\r
- }\r
- }\r
-\r
- if(sortGroupAscending)\r
- setOrder(align,seqs);\r
- else\r
- setReverseOrder( align, vectorToArray(seqs));\r
-\r
- sortGroupAscending = ! sortGroupAscending;\r
- }\r
-\r
- private static SequenceI [] vectorToArray(Vector tmp) {\r
- SequenceI[] seqs = new SequenceI[tmp.size()];\r
-\r
- for (int i=0; i < tmp.size(); i++) {\r
- seqs[i] = (SequenceI)tmp.elementAt(i);\r
- }\r
- return seqs;\r
- }\r
-\r
- private static SequenceI [] vectorSubsetToArray(Vector tmp, Vector mask) {\r
- Vector seqs = new Vector();\r
- int i,m, p;\r
- boolean[] tmask = new boolean[m=mask.size()];\r
- for (i=0; i<m; i++)\r
- tmask[i] = true;\r
- for (i=0; i < tmp.size(); i++) {\r
- Object sq;\r
- if (mask.contains(sq=tmp.elementAt(i))) {\r
- tmask[mask.indexOf(sq)] = false;\r
- seqs.addElement(sq);\r
- m--;\r
- }\r
- }\r
- for (i=0; i<tmask.length; i++)\r
- if (tmask[i])\r
- seqs.addElement(mask.elementAt(i));\r
- return vectorToArray(seqs);\r
- }\r
-\r
-\r
- public static void sortBy(AlignmentI align, AlignmentOrder order) {\r
- // Get an order vector that is a proper permutation of the positions in align\r
- Vector tmp = order.getOrder();\r
- if (tmp.size()<align.getHeight())\r
- addStrays(align, tmp);\r
- setOrder(align, tmp);\r
- }\r
-\r
- static boolean sortTreeAscending = true;\r
-\r
- public static Vector getOrderByTree(AlignmentI align, NJTree tree) {\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
-\r
- if (tmp.size() < nSeq)\r
- {\r
- addStrays(align, tmp);\r
- }\r
- if (tmp.size() != nSeq)\r
- System.err.println("ERROR: tmp.size()="+tmp.size()+" != nseq="+nSeq+" in getOrderByTree");\r
-\r
- }\r
- return tmp;\r
- }\r
-\r
- public static void sortByTree(AlignmentI align, NJTree tree) {\r
- Vector tmp = getOrderByTree(align, tree);\r
- // tmp should properly permute align with tree.\r
- if(sortTreeAscending)\r
- setOrder(align,tmp);\r
- else\r
- setReverseOrder(align, vectorSubsetToArray(tmp, align.getSequences()));\r
-\r
- sortTreeAscending = !sortTreeAscending; // JBPNote: this is totally random - have to keep last tree sort ref ...\r
- }\r
-\r
- private static void addStrays(AlignmentI align, Vector seqs) {\r
- int nSeq = align.getHeight();\r
- for (int i=0;i<nSeq;i++) {\r
- if (!seqs.contains(align.getSequenceAt(i))) {\r
- seqs.addElement(align.getSequenceAt(i));\r
- }\r
- }\r
- if (nSeq != seqs.size()) {\r
- System.err.println("ERROR: Size still not right even after addStrays");\r
- }\r
- }\r
-\r
- public static Vector _sortByTree(SequenceNode node, Vector tmp, Vector seqset) {\r
- if (node == null) {return tmp;}\r
-\r
- SequenceNode left = (SequenceNode)node.left();\r
- SequenceNode right = (SequenceNode)node.right();\r
-\r
- if (left == null && right == null) {\r
- if (!node.isPlaceholder() && node.element()!=null)\r
- if (node.element() instanceof SequenceI)\r
- if (!tmp.contains(node.element()))\r
- tmp.addElement((SequenceI)node.element());\r
- return tmp;\r
-\r
- } else {\r
- _sortByTree(left,tmp, seqset);\r
- _sortByTree(right,tmp, seqset);\r
- }\r
- return tmp;\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
- float[] ids = new float[alignment.length];\r
- for (int i=0; i<alignment.length; i++)\r
- ids[i] = (new Float(alignment[i].getName().substring(8))).floatValue();\r
- jalview.util.QuickSort.sort(ids, alignment);\r
- }\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.util.MessageManager;
+import jalview.util.QuickSort;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+/**
+ * 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 boolean sortTreeAscending = true;
+
+ /**
+ * last Annotation Label used by sortByScore
+ */
+ private static String lastSortByScore;
+
+ private static boolean sortByScoreAscending = true;
+
+ /**
+ * compact representation of last arguments to SortByFeatureScore
+ */
+ private static String lastSortByFeatureScore;
+
+ private static boolean sortByFeatureScoreAscending = 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;
+ synchronized (asq = align.getSequences())
+ {
+ 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;
+ synchronized (algn = align.getSequences())
+ {
+ List<SequenceI> tmp = new ArrayList<SequenceI>();
+
+ 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<SequenceGroup>();
+
+ 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<SequenceI>();
+
+ 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<SequenceI>();
+ 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<SequenceI>();
+
+ 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("WARNING: tmp.size()=" + tmp.size() + " != nseq="
+ + nSeq
+ + " in getOrderByTree - tree contains sequences not in alignment");
+ }
+ }
+
+ 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, 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()));
+ }
+ }
+
+ /**
+ * 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, List<SequenceI> 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())) // && (seqset==null ||
+ // seqset.size()==0 ||
+ // seqset.contains(tmp)))
+ {
+ tmp.add((SequenceI) node.element());
+ }
+ }
+ }
+
+ return tmp;
+ }
+ else
+ {
+ _sortByTree(left, tmp, seqset);
+ _sortByTree(right, tmp, seqset);
+ }
+
+ 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] = (new Float(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 (lastSortByScore != scoreLabel)
+ {
+ lastSortByScore = 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 the alignment using the features on each sequence found between start
+ * and stop with the given featureLabel (and optional group qualifier)
+ *
+ * @param featureLabel
+ * (may not be null)
+ * @param groupLabel
+ * (may be null)
+ * @param start
+ * (-1 to include non-positional features)
+ * @param stop
+ * (-1 to only sort on non-positional features)
+ * @param alignment
+ * - aligned sequences containing features
+ * @param method
+ * - one of the string constants FEATURE_SCORE, FEATURE_LABEL,
+ * FEATURE_DENSITY
+ */
+ public static void sortByFeature(String featureLabel, String groupLabel,
+ int start, int stop, AlignmentI alignment, String method)
+ {
+ sortByFeature(
+ featureLabel == null ? null : Arrays.asList(new String[]
+ { featureLabel }),
+ groupLabel == null ? null : Arrays.asList(new String[]
+ { groupLabel }), start, stop, alignment, method);
+ }
+
+ private static boolean containsIgnoreCase(final String lab,
+ final List<String> labs)
+ {
+ if (labs == null)
+ {
+ return true;
+ }
+ if (lab == null)
+ {
+ return false;
+ }
+ for (String label : labs)
+ {
+ if (lab.equalsIgnoreCase(label))
+ {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ public static void sortByFeature(List<String> featureLabels,
+ List<String> groupLabels, int start, int stop,
+ AlignmentI alignment, String method)
+ {
+ if (method != FEATURE_SCORE && method != FEATURE_LABEL
+ && method != FEATURE_DENSITY)
+ {
+ throw new Error(MessageManager
+ .getString("error.implementation_error_sortbyfeature"));
+ }
+
+ boolean ignoreScore = method != FEATURE_SCORE;
+ StringBuffer scoreLabel = new StringBuffer();
+ scoreLabel.append(start + stop + method);
+ // This doesn't quite work yet - we'd like to have a canonical ordering that
+ // can be preserved from call to call
+ if (featureLabels != null)
+ {
+ for (String label : featureLabels)
+ {
+ scoreLabel.append(label);
+ }
+ }
+ if (groupLabels != null)
+ {
+ for (String label : groupLabels)
+ {
+ scoreLabel.append(label);
+ }
+ }
+
+ /*
+ * if resorting the same feature, toggle sort order
+ */
+ if (lastSortByFeatureScore == null
+ || !scoreLabel.toString().equals(lastSortByFeatureScore))
+ {
+ sortByFeatureScoreAscending = true;
+ }
+ else
+ {
+ sortByFeatureScoreAscending = !sortByFeatureScoreAscending;
+ }
+ lastSortByFeatureScore = scoreLabel.toString();
+
+ 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 = 0, max = 0;
+ for (int i = 0; i < seqs.length; i++)
+ {
+ SequenceFeature[] sf = seqs[i].getSequenceFeatures();
+ if (sf == null)
+ {
+ sf = new SequenceFeature[0];
+ }
+ else
+ {
+ SequenceFeature[] tmp = new SequenceFeature[sf.length];
+ for (int s = 0; s < tmp.length; s++)
+ {
+ tmp[s] = sf[s];
+ }
+ sf = tmp;
+ }
+ int sstart = (start == -1) ? start : seqs[i].findPosition(start);
+ int sstop = (stop == -1) ? stop : seqs[i].findPosition(stop);
+ seqScores[i] = 0;
+ scores[i] = 0.0;
+ int n = sf.length;
+ for (int f = 0; f < sf.length; f++)
+ {
+ // filter for selection criteria
+ SequenceFeature feature = sf[f];
+
+ /*
+ * double-check feature overlaps columns (JAL-2544)
+ * (could avoid this with a findPositions(fromCol, toCol) method)
+ * findIndex returns base 1 column values, startCol/endCol are base 0
+ */
+ boolean noOverlap = seqs[i].findIndex(feature.getBegin()) > stop + 1
+ || seqs[i].findIndex(feature.getEnd()) < start + 1;
+ boolean skipFeatureType = featureLabels != null && !AlignmentSorter
+ .containsIgnoreCase(feature.type, featureLabels);
+ boolean skipFeatureGroup = groupLabels != null
+ && (feature.getFeatureGroup() != null
+ && !AlignmentSorter.containsIgnoreCase(
+ feature.getFeatureGroup(), groupLabels));
+ if (noOverlap || skipFeatureType || skipFeatureGroup)
+ {
+ // forget about this feature
+ sf[f] = null;
+ n--;
+ }
+ else
+ {
+ // or, also take a look at the scores if necessary.
+ if (!ignoreScore && !Float.isNaN(feature.getScore()))
+ {
+ if (seqScores[i] == 0)
+ {
+ hasScores++;
+ }
+ seqScores[i]++;
+ hasScore[i] = true;
+ scores[i] += feature.getScore(); // take the first instance of this
+ // score.
+ }
+ }
+ }
+ SequenceFeature[] fs;
+ feats[i] = fs = new SequenceFeature[n];
+ if (n > 0)
+ {
+ n = 0;
+ for (int f = 0; f < sf.length; f++)
+ {
+ if (sf[f] != null)
+ {
+ ((SequenceFeature[]) feats[i])[n++] = sf[f];
+ }
+ }
+ if (method == FEATURE_LABEL)
+ {
+ // order the labels by alphabet
+ String[] labs = new String[fs.length];
+ for (int l = 0; l < labs.length; l++)
+ {
+ labs[l] = (fs[l].getDescription() != null
+ ? fs[l].getDescription()
+ : fs[l].getType());
+ }
+ QuickSort.sort(labs, ((Object[]) feats[i]));
+ }
+ }
+ if (hasScore[i])
+ {
+ // compute average score
+ scores[i] /= seqScores[i];
+ // update the score bounds.
+ if (hasScores == 1)
+ {
+ max = min = scores[i];
+ }
+ else
+ {
+ if (max < scores[i])
+ {
+ max = scores[i];
+ }
+ if (min > scores[i])
+ {
+ min = scores[i];
+ }
+ }
+ }
+ }
+
+ if (method == FEATURE_SCORE)
+ {
+ 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, sortByFeatureScoreAscending);
+ }
+ else if (method == FEATURE_DENSITY)
+ {
+ 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, sortByFeatureScoreAscending);
+ }
+ else
+ {
+ if (method == FEATURE_LABEL)
+ {
+ throw new Error(
+ MessageManager.getString("error.not_yet_implemented"));
+ }
+ }
+
+ setOrder(alignment, seqs);
+ }
+
+}