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] = (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.
+ *
+ * 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 featureTypes,
+ List 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 sfs = seqs[i].findFeatures(startCol + 1,
+ endCol + 1, types);
+
+ seqScores[i] = 0;
+ scores[i] = 0.0;
+
+ Iterator 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 featureTypes, List 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;
+ }
+
+}