s2.getDatasetSequence() == null ? s2 : s2.getDatasetSequence());
return alSeq2;
}
-
/**
* fraction of seq2 matched in the alignment
+ *
* @return NaN or [0..1]
*/
public double getS2Coverage()
match++;
}
}
+
+ /*
+ * we built the character strings backwards, so now
+ * reverse them to convert to sequence strings
+ */
+ astr1 = sb1.reverse().toString();
+ astr2 = sb2.reverse().toString();
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void traceAlignmentWithEndGaps()
+ {
+ // Find the maximum score along the rhs or bottom row
+ float max = -Float.MAX_VALUE;
+
+ for (int i = 0; i < seq1.length; i++)
+ {
+ if (score[i][seq2.length - 1] > max)
+ {
+ max = score[i][seq2.length - 1];
+ maxi = i;
+ maxj = seq2.length - 1;
+ }
+ }
+
+ for (int j = 0; j < seq2.length; j++)
+ {
+ if (score[seq1.length - 1][j] > max)
+ {
+ max = score[seq1.length - 1][j];
+ maxi = seq1.length - 1;
+ maxj = j;
+ }
+ }
+
+ int i = maxi;
+ int j = maxj;
+ int trace;
+ maxscore = score[i][j] / 10f;
+
+ // prepare trailing gaps
+ while ((i < seq1.length - 1) || (j < seq2.length - 1))
+ {
+ i++;
+ j++;
+ }
+ seq1end = i + 1;
+ seq2end = j + 1;
+
+ aseq1 = new int[seq1.length + seq2.length];
+ aseq2 = new int[seq1.length + seq2.length];
+
+ StringBuilder sb1 = new StringBuilder(aseq1.length);
+ StringBuilder sb2 = new StringBuilder(aseq2.length);
+
+ count = (seq1.length + seq2.length) - 1;
+
+ // get trailing gaps
+ while ((i >= seq1.length) || (j >= seq2.length))
+ {
+ if (i >= seq1.length)
+ {
+ aseq1[count] = GAP_INDEX;
+ sb1.append("-");
+ aseq2[count] = seq2[j];
+ sb2.append(s2str.charAt(j));
+ }
+ else if (j >= seq2.length)
+ {
+ aseq1[count] = seq1[i];
+ sb1.append(s1str.charAt(i));
+ aseq2[count] = GAP_INDEX;
+ sb2.append("-");
+ }
+ i--;
+ j--;
+ }
+
+ while (i > 0 && j > 0)
+ {
+ aseq1[count] = seq1[i];
+ sb1.append(s1str.charAt(i));
+ aseq2[count] = seq2[j];
+ sb2.append(s2str.charAt(j));
+
+ trace = findTrace(i, j);
+
+ if (trace == 0)
+ {
+ i--;
+ j--;
+ }
+ else if (trace == 1)
+ {
+ j--;
+ aseq1[count] = GAP_INDEX;
+ sb1.replace(sb1.length() - 1, sb1.length(), "-");
+ }
+ else if (trace == -1)
+ {
+ i--;
+ aseq2[count] = GAP_INDEX;
+ sb2.replace(sb2.length() - 1, sb2.length(), "-");
+ }
+
+ count--;
+ }
+
+ seq1start = i + 1;
+ seq2start = j + 1;
+
+ aseq1[count] = seq1[i];
+ sb1.append(s1str.charAt(i));
+ aseq2[count] = seq2[j];
+ sb2.append(s2str.charAt(j));
+
+ // get initial gaps
+ while (j > 0 || i > 0)
+ {
+ if (j > 0)
+ {
+ j--;
+ sb1.append("-");
+ sb2.append(s2str.charAt(j));
+ }
+ else if (i > 0)
+ {
+ i--;
+ sb1.append(s1str.charAt(i));
+ sb2.append("-");
+ }
+ }
-
/*
* we built the character strings backwards, so now
* reverse them to convert to sequence strings
private final ScoreMatrix DNA;
+ private final ScoreMatrix FOLDSEEK3DI;
+
+ private final ScoreMatrix SECONDARYSTRUCTURE;
+
private static ScoreModels instance;
private Map<String, ScoreModelI> models;
* <li>PAM250</li>
* <li>PID</li>
* <li>DNA</li>
- * <li>Sequence Feature Similarity</li>
+ * <li>Sequence Feature Similarity</li> *
+ * <li>Secondary Structure Similarity</li>
++ * <li>FOLDSEEK_3di</li>
* </ul>
*/
private ScoreModels()
BLOSUM62 = loadScoreMatrix("scoreModel/blosum62.scm");
PAM250 = loadScoreMatrix("scoreModel/pam250.scm");
DNA = loadScoreMatrix("scoreModel/dna.scm");
+ FOLDSEEK3DI = loadScoreMatrix("scoreModel/foldseek_mat3di.scm");
registerScoreModel(new PIDModel());
registerScoreModel(new FeatureDistanceModel());
+ SECONDARYSTRUCTURE = loadScoreMatrix(
+ "scoreModel/secondarystructure.scm");
++ // JBPNote - this overwrites previous
+ registerScoreModel(new SecondaryStructureDistanceModel());
+
}
/**
{
return PAM250;
}
+
+ public ScoreMatrix getSecondaryStructureMatrix()
+ {
+ return SECONDARYSTRUCTURE;
+ }
++
+ public ScoreMatrix getFOLDSEEK3DI()
+ {
+ return FOLDSEEK3DI;
+ }
-
}
*/
Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly);
+ /**
+ * notify all concerned that the alignment data has changed and derived data
+ * needs to be recalculated
+ */
+ public void notifyAlignmentChanged();
+
+ /**
+ * retrieve a matrix associated with the view's alignment's annotation
+ *
+ * @param alignmentAnnotation
+ * @return contact matrix or NULL
+ */
ContactMatrixI getContactMatrix(AlignmentAnnotation alignmentAnnotation);
-
+ ProfilesI getSequenceSSConsensusHash();
+ boolean is3di();
+
+ public AlignmentAnnotation getComparisonAnnotation();
}
protected void calculate_actionPerformed()
{
boolean doPCA = pca.isSelected();
- String modelName = modelNames.getSelectedItem().toString();
+ boolean doPaSiMap = pasimap.isSelected();
+ boolean doPairwise = pairwise.isSelected();
+ String modelName = modelNames.getSelectedItem() == null ? ""
+ : modelNames.getSelectedItem().toString();
+ String ssSource = "";
+ Object selectedItem = ssSourceDropdown.getSelectedItem();
+ if (selectedItem != null)
+ {
+ ssSource = selectedItem.toString();
+ }
- SimilarityParams params = getSimilarityParameters(doPCA);
+ SimilarityParamsI params = getSimilarityParameters(doPCA);
+ if (ssSource.length() > 0)
+ {
+ params.setSecondaryStructureSource(ssSource);
+ }
if (doPCA)
{
{
continue;
}
- if (params!=null)
-
++ if (sm!=null)
+ {
- as.setScoreMatrix(params);
++ as.setScoreMatrix(sm);
+ }
as.calcScoreMatrix();
- as.traceAlignment();
+ if (endGaps)
+ {
+ as.traceAlignmentWithEndGaps();
+ }
+ else
+ {
+ as.traceAlignment();
+ }
+ as.scoreAlignment();
- if (!first)
+ if (!first && !quiet)
{
jalview.bin.Console.outPrintln(DASHES);
textarea.append(DASHES);
import jalview.util.MessageManager;
import jalview.viewmodel.styles.ViewStyle;
import jalview.workers.AlignCalcManager;
+import jalview.workers.AlignmentComparisonThread;
import jalview.workers.ComplementConsensusThread;
import jalview.workers.ConsensusThread;
+ import jalview.workers.SecondaryStructureConsensusThread;
import jalview.workers.StrucConsensusThread;
/**
}
}
}
+ if (getCodingComplement() != null)
+ {
+ if (getCodingComplement().isNucleotide() == isNucleotide())
+ {
+ if (calculator.getRegisteredWorkersOfClass(
+ AlignmentComparisonThread.class) == null)
+ {
+ initAlignmentComparison(ap);
+ ap.adjustAnnotationHeight();
+ }
+ }
+ }
}
+ /**
+ * trigger update of consensus annotation
+ */
+ public void updateSecondaryStructureConsensus(final AlignmentViewPanel ap)
+ {
+ // see note in mantis : issue number 8585
+ if (secondaryStructureConsensus == null || !autoCalculateConsensus)
+ {
+ return;
+ }
+ if (calculator.getRegisteredWorkersOfClass(
+ SecondaryStructureConsensusThread.class) == null)
+ {
+ calculator.registerWorker(
+ new SecondaryStructureConsensusThread(this, ap));
+ }
+ }
+
// --------START Structure Conservation
public void updateStrucConsensus(final AlignmentViewPanel ap)
{
* peptide models for PCA
*/
List<ScoreModelI> filtered = CalculationChooser
- .getApplicableScoreModels(false, true);
- assertEquals(filtered.size(), 5);
+ .getApplicableScoreModels(false, true, true, false);
- assertEquals(filtered.size(), 5);
++ assertEquals(filtered.size(), 6);
assertSame(filtered.get(0), blosum62);
assertSame(filtered.get(1), pam250);
- assertEquals(filtered.get(2).getName(), "PID");
- assertEquals(filtered.get(3).getName(), "Sequence Feature Similarity");
- assertEquals(filtered.get(4).getName(),
+ assertEquals(filtered.get(2).getName(), "Mat3di");
+ assertEquals(filtered.get(4).getName(), "Sequence Feature Similarity");
++ assertEquals(filtered.get(5).getName(),
+ "Secondary Structure Similarity");
/*
* peptide models for Tree are the same
*/
- filtered = CalculationChooser.getApplicableScoreModels(false, false);
- assertEquals(filtered.size(), 5);
+ filtered = CalculationChooser.getApplicableScoreModels(false, false,
+ true, false);
- assertEquals(filtered.size(), 5);
++ assertEquals(filtered.size(), 6);
++
assertSame(filtered.get(0), blosum62);
assertSame(filtered.get(1), pam250);
- assertEquals(filtered.get(2).getName(), "PID");
- assertEquals(filtered.get(3).getName(), "Sequence Feature Similarity");
+ assertEquals(filtered.get(2).getName(), "Mat3di");
+ assertEquals(filtered.get(3).getName(), "PID");
+ assertEquals(filtered.get(4).getName(), "Sequence Feature Similarity");
+ assertEquals(filtered.get(4).getName(),
+ "Secondary Structure Similarity");
+
+
/*
* nucleotide models for PCA
*/
/*
* nucleotide models for Tree are unchanged
*/
- filtered = CalculationChooser.getApplicableScoreModels(true, false);
+ filtered = CalculationChooser.getApplicableScoreModels(true, false,
+ true, false);
- assertEquals(filtered.size(), 4);
+ assertEquals(filtered.size(), 3);
assertSame(filtered.get(0), dna);
assertEquals(filtered.get(1).getName(), "PID");
assertEquals(filtered.get(2).getName(), "Sequence Feature Similarity");
git://source.jalview.org / jalview.git / commitdiff