import jalview.datamodel.Annotation;
import jalview.datamodel.Profile;
import jalview.datamodel.ProfileI;
+import jalview.datamodel.Profiles;
+import jalview.datamodel.ProfilesI;
import jalview.datamodel.ResidueCount;
-import jalview.datamodel.SequenceI;
import jalview.datamodel.ResidueCount.SymbolCounts;
+import jalview.datamodel.SequenceI;
import jalview.ext.android.SparseIntArray;
import jalview.util.Comparison;
import jalview.util.Format;
import jalview.util.MappingUtils;
import jalview.util.QuickSort;
+import java.awt.Color;
import java.util.Arrays;
import java.util.Hashtable;
import java.util.List;
}
}
- public static final ProfileI[] calculate(List<SequenceI> list,
- int start, int end)
+ public static final ProfilesI calculate(List<SequenceI> list, int start,
+ int end)
{
return calculate(list, start, end, false);
}
- public static final ProfileI[] calculate(List<SequenceI> sequences,
+ public static final ProfilesI calculate(List<SequenceI> sequences,
int start, int end, boolean profile)
{
SequenceI[] seqs = new SequenceI[sequences.size()];
for (int i = 0; i < sequences.size(); i++)
{
seqs[i] = sequences.get(i);
- if (seqs[i].getLength() > width)
+ int length = seqs[i].getLength();
+ if (length > width)
{
- width = seqs[i].getLength();
+ width = length;
}
}
- ProfileI[] reply = new ProfileI[width];
-
if (end >= width)
{
end = width;
}
- calculate(seqs, start, end, reply, profile);
+ ProfilesI reply = calculate(seqs, width, start, end, profile);
return reply;
}
}
* Calculate the consensus symbol(s) for each column in the given range.
*
* @param sequences
+ * @param width
+ * the full width of the alignment
* @param start
* start column (inclusive, base zero)
* @param end
* end column (exclusive)
- * @param result
- * array in which to store profile per column
* @param saveFullProfile
* if true, store all symbol counts
*/
- public static final void calculate(final SequenceI[] sequences,
- int start, int end, ProfileI[] result, boolean saveFullProfile)
+ public static final ProfilesI calculate(final SequenceI[] sequences,
+ int width, int start, int end, boolean saveFullProfile)
{
// long now = System.currentTimeMillis();
int seqCount = sequences.length;
int nucleotideCount = 0;
int peptideCount = 0;
+ ProfileI[] result = new ProfileI[width];
+
for (int column = start; column < end; column++)
{
/*
result[column] = profile;
}
+ return new Profiles(result);
// long elapsed = System.currentTimeMillis() - now;
// System.out.println(elapsed);
}
* the annotation row to add annotations to
* @param profiles
* the source consensus data
- * @param iStart
- * start column
- * @param width
- * end column
+ * @param startCol
+ * start column (inclusive)
+ * @param endCol
+ * end column (exclusive)
* @param ignoreGaps
* if true, normalise residue percentages ignoring gaps
* @param showSequenceLogo
* number of sequences
*/
public static void completeConsensus(AlignmentAnnotation consensus,
- ProfileI[] profiles, int iStart, int width, boolean ignoreGaps,
+ ProfilesI profiles, int startCol, int endCol, boolean ignoreGaps,
boolean showSequenceLogo, long nseq)
{
// long now = System.currentTimeMillis();
if (consensus == null || consensus.annotations == null
- || consensus.annotations.length < width)
+ || consensus.annotations.length < endCol)
{
/*
* called with a bad alignment annotation row
return;
}
- final int dp = getPercentageDp(nseq);
-
- for (int i = iStart; i < width; i++)
+ for (int i = startCol; i < endCol; i++)
{
- ProfileI profile;
- if (i >= profiles.length || ((profile = profiles[i]) == null))
+ ProfileI profile = profiles.get(i);
+ if (profile == null)
{
/*
* happens if sequences calculated over were
* shorter than alignment width
*/
consensus.annotations[i] = null;
- continue;
+ return;
}
+ final int dp = getPercentageDp(nseq);
+
float value = profile.getPercentageIdentity(ignoreGaps);
String description = getTooltip(profile, value, showSequenceLogo,
{
modalResidue = "+";
}
- consensus.annotations[i] = new Annotation(modalResidue,
- description, ' ', value);
+ consensus.annotations[i] = new Annotation(modalResidue, description,
+ ' ', value);
}
// long elapsed = System.currentTimeMillis() - now;
// System.out.println(-elapsed);
}
/**
+ * Derive the gap count annotation row.
+ *
+ * @param gaprow
+ * the annotation row to add annotations to
+ * @param profiles
+ * the source consensus data
+ * @param startCol
+ * start column (inclusive)
+ * @param endCol
+ * end column (exclusive)
+ */
+ public static void completeGapAnnot(AlignmentAnnotation gaprow,
+ ProfilesI profiles, int startCol, int endCol, long nseq)
+ {
+ if (gaprow == null || gaprow.annotations == null
+ || gaprow.annotations.length < endCol)
+ {
+ /*
+ * called with a bad alignment annotation row
+ * wait for it to be initialised properly
+ */
+ return;
+ }
+ // always set ranges again
+ gaprow.graphMax = nseq;
+ gaprow.graphMin = 0;
+ double scale = 0.8/nseq;
+ for (int i = startCol; i < endCol; i++)
+ {
+ ProfileI profile = profiles.get(i);
+ if (profile == null)
+ {
+ /*
+ * happens if sequences calculated over were
+ * shorter than alignment width
+ */
+ gaprow.annotations[i] = null;
+ return;
+ }
+
+ final int gapped = profile.getNonGapped();
+
+ String description = "" + gapped;
+
+ gaprow.annotations[i] = new Annotation("", description,
+ '\0', gapped, jalview.util.ColorUtils.bleachColour(
+ Color.DARK_GRAY, (float) scale * gapped));
+ }
+ }
+
+ /**
* Returns a tooltip showing either
* <ul>
* <li>the full profile (percentages of all residues present), if
* calculations
* @return
*/
- public static int[] extractProfile(ProfileI profile,
- boolean ignoreGaps)
+ public static int[] extractProfile(ProfileI profile, boolean ignoreGaps)
{
int[] rtnval = new int[64];
ResidueCount counts = profile.getCounts();