static boolean sortTreeAscending = true;
+ /**
+ * last Annotation Label used by sortByScore
+ */
private static String lastSortByScore;
/**
+ * compact representation of last arguments to SortByFeatureScore
+ */
+ private static String lastSortByFeatureScore;
+
+ /**
* Sort by Percentage Identity w.r.t. s
*
* @param align
{
if (!hasScore[i])
{
- scores[i] = (max + i);
+ scores[i] = (max + i+1.0);
}
}
}
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 : 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)
+ {
+ 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);
+ 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]);
+ }
+ 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 && 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);
+ seqScores[i]=0;
+ scores[i]=0.0;
+ int n=sf.length;
+ for (int f=0;f<sf.length;f++)
+ {
+ // 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
+ && (sf[f].getFeatureGroup() == null
+ || !AlignmentSorter.containsIgnoreCase(sf[f].getFeatureGroup(), groupLabels))))
+ {
+ // forget about this feature
+ sf[f] = null;
+ n--;
+ } else {
+ // or, also take a look at the scores if necessary.
+ if (!ignoreScore && sf[f].getScore()!=Float.NaN)
+ {
+ if (seqScores[i]==0)
+ {
+ hasScores++;
+ }
+ seqScores[i]++;
+ hasScore[i] = true;
+ scores[i] += sf[f].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());
+ }
+ jalview.util.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 + i);
+ }
+ }
+ }
+
+ jalview.util.QuickSort.sort(scores, seqs);
+ }
+ else
+ if (method==FEATURE_DENSITY)
+ {
+
+ // 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));
+ System.err.println("Sorting on Density: seq "+seqs[i].getName()+ " Feats: "+nf+" Score : "+scores[i]);
+ }
+ jalview.util.QuickSort.sort(scores, seqs);
+ }
+ else {
+ if (method==FEATURE_LABEL)
+ {
+ throw new Error("Not yet implemented.");
+ }
+ }
+ if (lastSortByFeatureScore ==null || scoreLabel.equals(lastSortByFeatureScore))
+ {
+ setOrder(alignment, seqs);
+ }
+ else
+ {
+ setReverseOrder(alignment, seqs);
+ }
+ lastSortByFeatureScore = scoreLabel.toString();
+ }
+
}
git://source.jalview.org / jalview.git / commitdiff