tmp)
{
if (node == null)
{
@@ -574,7 +623,7 @@ public class AlignmentSorter
// seqset.size()==0 ||
// seqset.contains(tmp)))
{
- tmp.addElement(node.element());
+ tmp.add((SequenceI) node.element());
}
}
}
@@ -583,13 +632,15 @@ public class AlignmentSorter
}
else
{
- _sortByTree(left, tmp, seqset);
- _sortByTree(right, tmp, seqset);
+ _sortByTree(left, tmp);
+ _sortByTree(right, tmp);
}
return tmp;
}
+
+
// Ordering Objects
// Alignment.sortBy(OrderObj) - sequence of sequence pointer refs in
// appropriate order
@@ -605,7 +656,7 @@ public class AlignmentSorter
for (int i = 0; i < alignment.length; i++)
{
- ids[i] = (new Float(alignment[i].getName().substring(8)))
+ ids[i] = (Float.valueOf(alignment[i].getName().substring(8)))
.floatValue();
}
@@ -615,7 +666,7 @@ public class AlignmentSorter
/**
* 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.
@@ -677,9 +728,9 @@ public class AlignmentSorter
}
jalview.util.QuickSort.sort(scores, seqs);
- if (lastSortByScore != scoreLabel)
+ if (lastSortByAnnotation != scoreLabel)
{
- lastSortByScore = scoreLabel;
+ lastSortByAnnotation = scoreLabel;
setOrder(alignment, seqs);
}
else
@@ -701,76 +752,42 @@ public class AlignmentSorter
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)
+ * 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
- * - aligned sequences containing features
+ * the alignment to be sorted
* @param method
- * - one of the string constants FEATURE_SCORE, FEATURE_LABEL,
- * FEATURE_DENSITY
+ * either "average_score" or "density" ("text" not yet implemented)
*/
- public static void sortByFeature(String featureLabel, String groupLabel,
- int start, int stop, AlignmentI alignment, String method)
- {
- sortByFeature(featureLabel == null ? null : new String[]
- { featureLabel }, groupLabel == null ? null : new String[]
- { groupLabel }, start, stop, alignment, method);
- }
-
- private static boolean containsIgnoreCase(final String lab,
- final String[] labs)
- {
- if (labs == null)
- {
- return true;
- }
- if (lab == null)
- {
- return false;
- }
- for (int q = 0; q < labs.length; q++)
- {
- if (labs[q] != null && lab.equalsIgnoreCase(labs[q]))
- {
- return true;
- }
- }
- return false;
- }
-
- public static void sortByFeature(String[] featureLabels,
- String[] groupLabels, int start, int stop, AlignmentI alignment,
- String method)
+ 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)
{
- throw new Error(
- "Implementation Error - sortByFeature method must be one of FEATURE_SCORE, FEATURE_LABEL or FEATURE_DENSITY.");
- }
- 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
- for (int i = 0; featureLabels != null && i < featureLabels.length; i++)
- {
- scoreLabel.append(featureLabels[i] == null ? "null"
- : featureLabels[i]);
- }
- for (int i = 0; groupLabels != null && i < groupLabels.length; i++)
- {
- scoreLabel.append(groupLabels[i] == null ? "null" : groupLabels[i]);
+ 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
@@ -778,56 +795,44 @@ public class AlignmentSorter
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;
+ Object[][] feats = new Object[seqs.length][];
+ double min = 0d;
+ double max = 0d;
+
for (int i = 0; i < seqs.length; i++)
{
- SequenceFeature[] sf = seqs[i].getSequenceFeatures();
- if (sf == null && seqs[i].getDatasetSequence() != null)
- {
- sf = seqs[i].getDatasetSequence().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);
+ /*
+ * 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;
- int n = sf.length;
- for (int f = 0; f < sf.length; f++)
+
+ Iterator it = sfs.listIterator();
+ while (it.hasNext())
{
- // filter for selection criteria
- if (
- // ignore features outwith alignment start-stop positions.
- (sf[f].end < sstart || sf[f].begin > sstop) ||
- // or ignore based on selection criteria
- (featureLabels != null && !AlignmentSorter
- .containsIgnoreCase(sf[f].type, featureLabels))
- || (groupLabels != null
- // problem here: we cannot eliminate null feature group features
- && (sf[f].getFeatureGroup() != null && !AlignmentSorter
- .containsIgnoreCase(sf[f].getFeatureGroup(),
- groupLabels))))
+ 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))
{
- // forget about this feature
- sf[f] = null;
- n--;
+ it.remove();
}
else
{
- // or, also take a look at the scores if necessary.
- if (!ignoreScore && sf[f].getScore() != Float.NaN)
+ float score = sf.getScore();
+ if (FEATURE_SCORE.equals(method) && !Float.isNaN(score))
{
if (seqScores[i] == 0)
{
@@ -835,33 +840,26 @@ public class AlignmentSorter
}
seqScores[i]++;
hasScore[i] = true;
- scores[i] += sf[f].getScore(); // take the first instance of this
- // score.
+ scores[i] += score;
+ // take the first instance of this score // ??
}
}
}
- SequenceFeature[] fs;
- feats[i] = fs = new SequenceFeature[n];
- if (n > 0)
+
+ feats[i] = sfs.toArray(new SequenceFeature[sfs.size()]);
+ if (!sfs.isEmpty())
{
- 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++)
+ // order the labels by alphabet (not yet implemented)
+ String[] labs = new String[sfs.size()];
+ for (int l = 0; l < sfs.size(); l++)
{
- labs[l] = (fs[l].getDescription() != null ? fs[l]
- .getDescription() : fs[l].getType());
+ SequenceFeature sf = sfs.get(l);
+ String description = sf.getDescription();
+ labs[l] = (description != null ? description : sf.getType());
}
- jalview.util.QuickSort.sort(labs, ((Object[]) feats[i]));
+ QuickSort.sort(labs, feats[i]);
}
}
if (hasScore[i])
@@ -871,23 +869,18 @@ public class AlignmentSorter
// update the score bounds.
if (hasScores == 1)
{
- max = min = scores[i];
+ min = scores[i];
+ max = min;
}
else
{
- if (max < scores[i])
- {
- max = scores[i];
- }
- if (min > scores[i])
- {
- min = scores[i];
- }
+ max = Math.max(max, scores[i]);
+ min = Math.min(min, scores[i]);
}
}
}
- if (method == FEATURE_SCORE)
+ if (FEATURE_SCORE.equals(method))
{
if (hasScores == 0)
{
@@ -904,58 +897,73 @@ public class AlignmentSorter
}
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]);
+ // 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]);
}
}
}
-
- jalview.util.QuickSort.sort(scores, seqs);
+ QuickSort.sortByDouble(scores, seqs, sortByFeatureAscending);
}
- else if (method == FEATURE_DENSITY)
+ else if (FEATURE_DENSITY.equals(method))
{
-
- // break ties between equivalent numbers for adjacent sequences by adding
- // 1/Nseq*i on the original order
- double fr = 0.9 / (1.0 * seqs.length);
for (int i = 0; i < seqs.length; i++)
{
- double nf;
- scores[i] = (0.05 + fr * i)
- + (nf = ((feats[i] == null) ? 0.0
- : 1.0 * ((SequenceFeature[]) feats[i]).length));
+ int featureCount = feats[i] == null ? 0
+ : ((SequenceFeature[]) feats[i]).length;
+ scores[i] = featureCount;
// System.err.println("Sorting on Density: seq "+seqs[i].getName()+
- // " Feats: "+nf+" Score : "+scores[i]);
+ // " Feats: "+featureCount+" Score : "+scores[i]);
}
- jalview.util.QuickSort.sort(scores, seqs);
+ QuickSort.sortByDouble(scores, seqs, sortByFeatureAscending);
}
- else
- {
- if (method == FEATURE_LABEL)
- {
- throw new Error("Not yet implemented.");
- }
- }
- if (lastSortByFeatureScore == null
- || !scoreLabel.toString().equals(lastSortByFeatureScore))
+
+ 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)
{
- sortByFeatureScoreAscending = true;
+ Collections.sort(featureTypes);
+ sb.append(featureTypes.toString());
}
- else
+ if (groups != null)
{
- sortByFeatureScoreAscending = !sortByFeatureScoreAscending;
+ Collections.sort(groups);
+ sb.append(groups.toString());
}
- if (sortByFeatureScoreAscending)
+ String scoreCriteria = sb.toString();
+
+ /*
+ * if resorting on the same criteria, toggle sort order
+ */
+ if (sortByFeatureCriteria == null
+ || !scoreCriteria.equals(sortByFeatureCriteria))
{
- setOrder(alignment, seqs);
+ sortByFeatureAscending = true;
}
else
{
- setReverseOrder(alignment, seqs);
+ sortByFeatureAscending = !sortByFeatureAscending;
}
- lastSortByFeatureScore = scoreLabel.toString();
+ sortByFeatureCriteria = scoreCriteria;
}
}