- if (method!=AlignmentSorter.FEATURE_SCORE && method!=AlignmentSorter.FEATURE_LABEL && method!=AlignmentSorter.FEATURE_DENSITY)
- {
- throw new Error("Implementation Error - sortByFeature method must be one of FEATURE_SCORE, FEATURE_LABEL or FEATURE_DENSITY.");
- }
- boolean ignoreScore=method!=AlignmentSorter.FEATURE_SCORE;
- StringBuffer scoreLabel = new StringBuffer();
- scoreLabel.append(start+stop+method);
- // This doesn't 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]);
- }
- 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
- // problem here: we cannot eliminate null feature group features
- && (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);
- } 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]);
- }
- }
- }
-
- 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(); */
+ * if (method!=AlignmentSorter.FEATURE_SCORE &&
+ * method!=AlignmentSorter.FEATURE_LABEL &&
+ * method!=AlignmentSorter.FEATURE_DENSITY) { throw newError(
+ * "Implementation Error - sortByFeature method must be one of FEATURE_SCORE, FEATURE_LABEL or FEATURE_DENSITY."
+ * ); } boolean ignoreScore=method!=AlignmentSorter.FEATURE_SCORE;
+ * StringBuffer scoreLabel = new StringBuffer();
+ * scoreLabel.append(start+stop+method); // This doesn't 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]); }
+ * 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 // problem here: we cannot eliminate null feature
+ * group features && (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); } 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]); } } }
+ *
+ * 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();
+ */