/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
+ * 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.
- *
- * This program 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.
- *
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
-import java.util.*;
-
-import jalview.datamodel.*;
-import jalview.util.*;
-
-/**
- * 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)
+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.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 NJTree lastTree = null;
+
+ static TreeModel lastTree = null;
+
static boolean sortTreeAscending = true;
+
+ /**
+ * last Annotation Label used by sortByScore
+ */
private static String lastSortByScore;
+ private static boolean sortByScoreAscending = true;
+
/**
- * Sort by Percentage Identity w.r.t. s
- *
- * @param align AlignmentI
- * @param s SequenceI
- * @param tosort sequences from align that are to be sorted.
+ * compact representation of last arguments to SortByFeatureScore
*/
- public static void sortByPID(AlignmentI align, SequenceI s, SequenceI[] tosort)
+ 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] = Comparison.PID(align.getSequenceAt(i).getSequenceAsString(),
- s.getSequenceAsString());
+ scores[i] = (float) PIDModel.computePID(align.getSequenceAt(i)
+ .getSequenceAsString(), refSeq, pidParams);
seqs[i] = align.getSequenceAt(i);
}
- QuickSort.sort(scores, 0, scores.length - 1, seqs);
+ QuickSort.sort(scores, seqs);
setReverseOrder(align, seqs);
}
/**
* Reverse the order of the sort
- *
- * @param align DOCUMENT ME!
- * @param seqs DOCUMENT ME!
+ *
+ * @param align
+ * DOCUMENT ME!
+ * @param seqs
+ * DOCUMENT ME!
*/
private static void setReverseOrder(AlignmentI align, SequenceI[] seqs)
{
int len = 0;
- if ( (nSeq % 2) == 0)
+ if ((nSeq % 2) == 0)
{
len = nSeq / 2;
}
}
// NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
- for (int i = 0; i < len; i++)
+ List<SequenceI> asq;
+ synchronized (asq = align.getSequences())
{
- //SequenceI tmp = seqs[i];
- align.getSequences().setElementAt(seqs[nSeq - i - 1], i);
- align.getSequences().setElementAt(seqs[i], nSeq - i - 1);
+ 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
+ *
+ * @param align
+ * Alignment object to be updated
+ * @param tmp
+ * sequences as a vector
*/
- private static void setOrder(AlignmentI align, Vector tmp)
+ 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
+ *
+ * @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
- Vector algn = align.getSequences();
- Vector tmp = new Vector();
-
- for (int i = 0; i < seqs.length; i++)
+ List<SequenceI> algn;
+ synchronized (algn = align.getSequences())
{
- if (algn.contains(seqs[i]))
+ List<SequenceI> tmp = new ArrayList<SequenceI>();
+
+ for (int i = 0; i < seqs.length; i++)
{
- tmp.addElement(seqs[i]);
+ if (algn.contains(seqs[i]))
+ {
+ tmp.add(seqs[i]);
+ }
}
- }
- algn.removeAllElements();
- //User may have hidden seqs, then clicked undo or redo
- for (int i = 0; i < tmp.size(); i++)
- {
- algn.addElement(tmp.elementAt(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
+ *
+ * @param align
+ * The alignment object to sort
*/
public static void sortByID(AlignmentI align)
{
}
/**
- * 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
+ * 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
- Vector groups = new Vector();
+ // MAINTAINS ORIGNAL SEQUENCE ORDER,
+ // ORDERS BY GROUP SIZE
+ List<SequenceGroup> groups = new ArrayList<SequenceGroup>();
if (groups.hashCode() != lastGroupHash)
{
sortGroupAscending = !sortGroupAscending;
}
- //SORTS GROUPS BY SIZE
- //////////////////////
- for (int i = 0; i < align.getGroups().size(); i++)
+ // SORTS GROUPS BY SIZE
+ // ////////////////////
+ for (SequenceGroup sg : align.getGroups())
{
- SequenceGroup sg = (SequenceGroup) align.getGroups().elementAt(i);
-
for (int j = 0; j < groups.size(); j++)
{
- SequenceGroup sg2 = (SequenceGroup) groups.elementAt(j);
+ SequenceGroup sg2 = groups.get(j);
if (sg.getSize() > sg2.getSize())
{
- groups.insertElementAt(sg, j);
+ groups.add(j, sg);
break;
}
if (!groups.contains(sg))
{
- groups.addElement(sg);
+ groups.add(sg);
}
}
- //NOW ADD SEQUENCES MAINTAINING ALIGNMENT ORDER
- ///////////////////////////////////////////////
- Vector seqs = new Vector();
+ // NOW ADD SEQUENCES MAINTAINING ALIGNMENT ORDER
+ // /////////////////////////////////////////////
+ List<SequenceI> seqs = new ArrayList<SequenceI>();
for (int i = 0; i < groups.size(); i++)
{
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+ SequenceGroup sg = groups.get(i);
SequenceI[] orderedseqs = sg.getSequencesInOrder(align);
for (int j = 0; j < orderedseqs.length; j++)
{
- seqs.addElement(orderedseqs[j]);
+ seqs.add(orderedseqs[j]);
}
}
else
{
setReverseOrder(align,
- vectorSubsetToArray(seqs, align.getSequences()));
+ vectorSubsetToArray(seqs, align.getSequences()));
}
}
/**
- * Converts Vector to array.
- * java 1.18 does not have Vector.toArray()
- *
- * @param tmp Vector of SequenceI objects
- *
- * @return array of Sequence[]
+ * 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[] vectorToArray(Vector tmp)
+ private static SequenceI[] vectorSubsetToArray(List<SequenceI> tmp,
+ List<SequenceI> mask)
{
- SequenceI[] seqs = new SequenceI[tmp.size()];
-
- for (int i = 0; i < tmp.size(); i++)
- {
- seqs[i] = (SequenceI) tmp.elementAt(i);
- }
+ // or?
+ // tmp2 = tmp.retainAll(mask);
+ // return tmp2.addAll(mask.removeAll(tmp2))
- return seqs;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param tmp DOCUMENT ME!
- * @param mask DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- private static SequenceI[] vectorSubsetToArray(Vector tmp, Vector mask)
- {
- Vector seqs = new Vector();
- int i;
+ ArrayList<SequenceI> seqs = new ArrayList<SequenceI>();
+ int i, idx;
boolean[] tmask = new boolean[mask.size()];
for (i = 0; i < mask.size(); i++)
for (i = 0; i < tmp.size(); i++)
{
- Object sq = tmp.elementAt(i);
-
- if (mask.contains(sq) && tmask[mask.indexOf(sq)])
+ SequenceI sq = tmp.get(i);
+ idx = mask.indexOf(sq);
+ if (idx > -1 && tmask[idx])
{
- tmask[mask.indexOf(sq)] = false;
- seqs.addElement(sq);
+ tmask[idx] = false;
+ seqs.add(sq);
}
}
{
if (tmask[i])
{
- seqs.addElement(mask.elementAt(i));
+ seqs.add(mask.get(i));
}
}
- return vectorToArray(seqs);
+ return seqs.toArray(new SequenceI[seqs.size()]);
}
/**
* Sorts by a given AlignmentOrder object
- *
- * @param align Alignment to order
- * @param order specified order for alignment
+ *
+ * @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
- Vector tmp = order.getOrder();
+ List<SequenceI> tmp = order.getOrder();
if (lastOrder == order)
{
}
else
{
- setReverseOrder(align,
- vectorSubsetToArray(tmp, align.getSequences()));
+ setReverseOrder(align, vectorSubsetToArray(tmp, align.getSequences()));
}
}
/**
* DOCUMENT ME!
- *
- * @param align alignment to order
- * @param tree tree which has
- *
+ *
+ * @param align
+ * alignment to order
+ * @param tree
+ * tree which has
+ *
* @return DOCUMENT ME!
*/
- private static Vector getOrderByTree(AlignmentI align, NJTree tree)
+ private static List<SequenceI> getOrderByTree(AlignmentI align,
+ TreeModel tree)
{
int nSeq = align.getHeight();
- Vector tmp = new Vector();
+ List<SequenceI> tmp = new ArrayList<SequenceI>();
tmp = _sortByTree(tree.getTopNode(), tmp, align.getSequences());
{
// 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)
+ // sequences)
+ if (tmp.size() != nSeq)
{
addStrays(align, tmp);
}
if (tmp.size() != nSeq)
{
- System.err.println("ERROR: tmp.size()=" + tmp.size() +
- " != nseq=" + nSeq + " in getOrderByTree");
+ System.err
+ .println("WARNING: tmp.size()="
+ + tmp.size()
+ + " != nseq="
+ + nSeq
+ + " in getOrderByTree - tree contains sequences not in alignment");
}
}
/**
* Sorts the alignment by a given tree
- *
- * @param align alignment to order
- * @param tree tree which has
+ *
+ * @param align
+ * alignment to order
+ * @param tree
+ * tree which has
*/
- public static void sortByTree(AlignmentI align, NJTree tree)
+ public static void sortByTree(AlignmentI align, TreeModel tree)
{
- Vector tmp = getOrderByTree(align, tree);
+ List<SequenceI> tmp = getOrderByTree(align, tree);
// tmp should properly permute align with tree.
if (lastTree != tree)
}
else
{
- setReverseOrder(align,
- vectorSubsetToArray(tmp, align.getSequences()));
+ setReverseOrder(align, vectorSubsetToArray(tmp, align.getSequences()));
}
}
/**
* DOCUMENT ME!
- *
- * @param align DOCUMENT ME!
- * @param seqs DOCUMENT ME!
+ *
+ * @param align
+ * DOCUMENT ME!
+ * @param tmp
+ * DOCUMENT ME!
*/
- private static void addStrays(AlignmentI align, Vector seqs)
+ private static void addStrays(AlignmentI align, List<SequenceI> tmp)
{
int nSeq = align.getHeight();
for (int i = 0; i < nSeq; i++)
{
- if (!seqs.contains(align.getSequenceAt(i)))
+ if (!tmp.contains(align.getSequenceAt(i)))
{
- seqs.addElement(align.getSequenceAt(i));
+ tmp.add(align.getSequenceAt(i));
}
}
- if (nSeq != seqs.size())
+ if (nSeq != tmp.size())
{
- System.err.println(
- "ERROR: Size still not right even after addStrays");
+ 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!
- *
+ *
+ * @param node
+ * DOCUMENT ME!
+ * @param tmp
+ * DOCUMENT ME!
+ * @param seqset
+ * DOCUMENT ME!
+ *
* @return DOCUMENT ME!
*/
- private static Vector _sortByTree(SequenceNode node, Vector tmp,
- Vector seqset)
+ private static List<SequenceI> _sortByTree(SequenceNode node,
+ List<SequenceI> tmp, List<SequenceI> seqset)
{
if (node == null)
{
SequenceNode left = (SequenceNode) node.left();
SequenceNode right = (SequenceNode) node.right();
- if ( (left == null) && (right == null))
+ if ((left == null) && (right == null))
{
if (!node.isPlaceholder() && (node.element() != null))
{
if (node.element() instanceof SequenceI)
{
- if (!tmp.contains(node.element()))
+ if (!tmp.contains(node.element())) // && (seqset==null ||
+ // seqset.size()==0 ||
+ // seqset.contains(tmp)))
{
- tmp.addElement( (SequenceI) node.element());
+ tmp.add((SequenceI) node.element());
}
}
}
}
// Ordering Objects
- // Alignment.sortBy(OrderObj) - sequence of sequence pointer refs in appropriate order
+ // Alignment.sortBy(OrderObj) - sequence of sequence pointer refs in
+ // appropriate order
//
/**
for (int i = 0; i < alignment.length; i++)
{
- ids[i] = (new Float(alignment[i].getName().substring(8))).floatValue();
+ 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
+ * 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)
+ 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
+ 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;
+ double min = 0, max = 0;
for (int i = 0; i < seqs.length; i++)
{
AlignmentAnnotation[] scoreAnn = seqs[i].getAnnotation(scoreLabel);
- if (scoreAnn!=null)
+ if (scoreAnn != null)
{
hasScores++;
hasScore[i] = true;
- scores[i] = scoreAnn[0].getScore(); // take the first instance of this score.
- if (hasScores==1)
+ scores[i] = scoreAnn[0].getScore(); // take the first instance of this
+ // score.
+ if (hasScores == 1)
{
max = min = scores[i];
- } else
+ }
+ else
{
- if (max<scores[i])
+ if (max < scores[i])
{
max = scores[i];
}
- if (min>scores[i])
+ if (min > scores[i])
{
min = scores[i];
}
hasScore[i] = false;
}
}
- if (hasScores==0)
+ if (hasScores == 0)
{
return; // do nothing - no scores present to sort by.
}
- if (hasScores<seqs.length)
+ if (hasScores < seqs.length)
{
- for (int i=0; i<seqs.length;i++)
+ for (int i = 0; i < seqs.length; i++)
{
if (!hasScore[i])
{
- scores[i] = (max+i);
+ scores[i] = (max + i + 1.0);
}
}
}
-
+
jalview.util.QuickSort.sort(scores, seqs);
- if (lastSortByScore!=scoreLabel)
+ if (lastSortByScore != scoreLabel)
{
lastSortByScore = scoreLabel;
setOrder(alignment, seqs);
- } else {
+ }
+ 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";
+
+ 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;
+ }
+
+ /**
+ * Sort sequences by feature score or density, optionally restricted by
+ * feature types, feature groups, or alignment start/end positions.
+ * <p>
+ * If the sort is repeated for the same combination of types and groups, sort
+ * order is reversed.
+ *
+ * @param featureLabels
+ * a list of feature types to include (or null for all)
+ * @param groupLabels
+ * a list of feature groups to include (or null for all)
+ * @param start
+ * start column position to include (base zero)
+ * @param stop
+ * 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<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
+ 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 && !Float.isNaN(sf[f].getScore()))
+ {
+ 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());
+ }
+ 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);
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff