import jalview.datamodel.SeqCigar;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequenceNode;
+import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
+import java.util.ArrayList;
import java.util.BitSet;
+import java.util.List;
import java.util.Vector;
public abstract class TreeBuilder extends TreeEngine
public static final String NEIGHBOUR_JOINING = "NJ";
protected SequenceI[] sequences;
+ protected List<String> labels;
public AlignmentView seqData;
}
init(seqStrings, start, end);
-
+
computeTree(sm, scoreParameters);
}
return sequences;
}
+
/**
*
* @return true if tree has real distances
*/
protected void computeTree(ScoreModelI sm, SimilarityParamsI scoreOptions)
{
+ labels = new ArrayList<String>();
+ sequences = sm.expandSeqData(sequences, seqData, scoreOptions, labels);
+ noseqs = sequences.length;
+
distances = sm.findDistances(seqData, scoreOptions);
makeLeaves();
SequenceNode sn = new SequenceNode();
sn.setElement(sequences[i]);
- sn.setName(sequences[i].getName());
+ if (labels.size()==noseqs)
+ {
+ sn.setName(labels.get(i));
+ } else {
+ sn.setName(sequences[i].getName());
+ }
node.addElement(sn);
BitSet bs = new BitSet();
bs.set(i);
import jalview.datamodel.SequenceI;
import jalview.math.Matrix;
import jalview.math.MatrixI;
+import jalview.util.Constants;
import jalview.util.MessageManager;
import java.util.ArrayList;
+import java.util.HashMap;
import java.util.HashSet;
+import java.util.List;
import java.util.Map;
import java.util.Set;
return true;
}
+ ArrayList<AlignmentAnnotation> ssForSeqs = null;
+
+ @Override
+ public SequenceI[] expandSeqData(SequenceI[] sequences,
+ AlignmentView seqData, SimilarityParamsI scoreParams,List<String> labels)
+ {
+ ssForSeqs = new ArrayList<AlignmentAnnotation>();
+ List<SequenceI> newSequences = new ArrayList<SequenceI>();
+ List<SeqCigar> newCigs = new ArrayList<SeqCigar>();
+ int sq = 0;
+
+
+
+ AlignmentAnnotation[] alignAnnotList = fr.getViewport().getAlignment()
+ .getAlignmentAnnotation();
+
+ String ssSource = scoreParams.getSecondaryStructureSource();
+ if(ssSource == null || ssSource == "") {
+ ssSource = MessageManager.getString("option.ss_providers_all");
+ }
+
+ /*
+ * Add secondary structure annotations that are added to the annotation track
+ * to the map
+ */
+ Map<SequenceI, ArrayList<AlignmentAnnotation>> ssAlignmentAnnotationForSequences
+ = AlignmentUtils.getSequenceAssociatedAlignmentAnnotations(alignAnnotList, ssSource);
+
+ for (SeqCigar scig : seqData.getSequences())
+ {
+ SequenceI alSeq = sequences[sq++];
+ List<AlignmentAnnotation> ssec = ssAlignmentAnnotationForSequences.get(scig.getRefSeq());
+ if (ssec == null)
+ {
+ // not defined
+ newSequences.add(alSeq);
+ labels.add(alSeq.getName()+"|"+" No Secondary Structure");
+ SeqCigar newSeqCigar = scig; //new SeqCigar(scig);
+ newCigs.add(newSeqCigar);
+ ssForSeqs.add(null);
+ } else {
+ for (int i = 0; i < ssec.size(); i++)
+ {
+ labels.add(alSeq.getName()+"|"+AlignmentUtils.extractSSSourceFromAnnotationDescription(ssec.get(i)));
+ //newSequences.add(seq);
+ newSequences.add(alSeq);
+ SeqCigar newSeqCigar = scig; // new SeqCigar(scig);
+ newCigs.add(newSeqCigar);
+ ssForSeqs.add(ssec.get(i));
+ }
+ }
+ }
+
+ seqData.setSequences(newCigs.toArray(new SeqCigar[0]));
+ return newSequences.toArray(new SequenceI[0]);
+
+ }
+
/**
* Calculates distance score [i][j] between each pair of protein sequences
* based on their secondary structure annotations (H, E, C).
@Override
public MatrixI findDistances(AlignmentView seqData,
SimilarityParamsI params)
- {
-
+ {
+ if (ssForSeqs==null || ssForSeqs.size()!=seqData.getSequences().length)
+ {
+ // expandSeqData needs to be called to initialise the hash
+ SequenceI[] sequences = new SequenceI[seqData.getSequences().length];
+ // we throw away the new labels in this case..
+ expandSeqData(sequences, seqData, params, new ArrayList<String>());
+ }
SeqCigar[] seqs = seqData.getSequences();
int noseqs = seqs.length; //no of sequences
int cpwidth = 0;
// need to get real position for view position
int[] viscont = seqData.getVisibleContigs();
-
- AlignmentAnnotation[] alignAnnotList = fr.getViewport().getAlignment()
- .getAlignmentAnnotation();
-
-
- /*
- * Add secondary structure annotations that are added to the annotation track
- * to the map
- */
- Map<SequenceI, ArrayList<AlignmentAnnotation>> ssAlignmentAnnotationForSequences
- = AlignmentUtils.getSequenceAssociatedAlignmentAnnotations(alignAnnotList, ssSource);
+
/*
* scan each column, compute and add to each similarity[i, j]
*/
for (int i = 0; i < (noseqs - 1); i++)
{
- //Iterates for each sequences
+ AlignmentAnnotation aa_i = ssForSeqs.get(i);
+ boolean undefinedSS1 = aa_i == null;
+ // check if the sequence contains gap in the current column
+ boolean gap1 = !seqsWithoutGapAtCol.contains(seqs[i]);
+ // secondary structure is fetched only if the current column is not
+ // gap for the sequence
+ char ss1 = '*';
+ if (!gap1 && !undefinedSS1)
+ {
+ // fetch the position in sequence for the column and finds the
+ // corresponding secondary structure annotation
+ // TO DO - consider based on priority and displayed
+ int seqPosition_i = seqs[i].findPosition(cpos);
+ if (aa_i != null)
+ ss1 = AlignmentUtils.findSSAnnotationForGivenSeqposition(aa_i,
+ seqPosition_i);
+ }
+ // Iterates for each sequences
for (int j = i + 1; j < noseqs; j++)
{
-
- //check if ss is defined
- boolean undefinedSS1 = ssAlignmentAnnotationForSequences.get(seqs[i].getRefSeq()) == null;
- boolean undefinedSS2 = ssAlignmentAnnotationForSequences.get(seqs[j].getRefSeq()) == null;
+
+ // check if ss is defined
+ AlignmentAnnotation aa_j = ssForSeqs.get(j);
+ boolean undefinedSS2 = aa_j == null;
// Set similarity to max score if both SS are not defined
- if (undefinedSS1 && undefinedSS2) {
- similarities[i][j] += ssRateMatrix.getMaximumScore();
- continue;
- }
-
+ if (undefinedSS1 && undefinedSS2)
+ {
+ similarities[i][j] += ssRateMatrix.getMaximumScore();
+ continue;
+ }
+
// Set similarity to minimum score if either one SS is not defined
- else if(undefinedSS1 || undefinedSS2) {
- similarities[i][j] += ssRateMatrix.getMinimumScore();
- continue;
+ else if (undefinedSS1 || undefinedSS2)
+ {
+ similarities[i][j] += ssRateMatrix.getMinimumScore();
+ continue;
}
-
- //check if the sequence contains gap in the current column
- boolean gap1 = !seqsWithoutGapAtCol.contains(seqs[i]);
- boolean gap2 = !seqsWithoutGapAtCol.contains(seqs[j]);
-
- //Variable to store secondary structure at the current column
- char ss1 = '*';
+
+ boolean gap2 = !seqsWithoutGapAtCol.contains(seqs[j]);
+
+ // Variable to store secondary structure at the current column
char ss2 = '*';
-
- //secondary structure is fetched only if the current column is not
- //gap for the sequence
- if(!gap1 && !undefinedSS1) {
- //fetch the position in sequence for the column and finds the
- //corresponding secondary structure annotation
- //TO DO - consider based on priority and displayed
- int seqPosition = seqs[i].findPosition(cpos);
- AlignmentAnnotation aa = ssAlignmentAnnotationForSequences.get(seqs[i].getRefSeq()).get(0);
- if(aa!=null)
- ss1 =
- AlignmentUtils.findSSAnnotationForGivenSeqposition(aa, seqPosition);
- }
-
- if(!gap2 && !undefinedSS2) {
+
+ if (!gap2 && !undefinedSS2)
+ {
int seqPosition = seqs[j].findPosition(cpos);
- AlignmentAnnotation aa = ssAlignmentAnnotationForSequences.get(seqs[j].getRefSeq()).get(0);
- if(aa!=null)
- ss2 =
- AlignmentUtils.findSSAnnotationForGivenSeqposition(aa, seqPosition);
- }
+
+ if (aa_j != null)
+ ss2 = AlignmentUtils.findSSAnnotationForGivenSeqposition(
+ aa_j, seqPosition);
+ }
if ((!gap1 && !gap2) || params.includeGaps())
{
// Calculate similarity score based on the substitution matrix
- double similarityScore = ssRateMatrix.getPairwiseScore(ss1, ss2);
+ double similarityScore = ssRateMatrix.getPairwiseScore(ss1,
+ ss2);
similarities[i][j] += similarityScore;
}
}
git://source.jalview.org / jalview.git / commitdiff