X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAAFrequency.java;h=892b1b1ff8cb4efc79cdb7f3bac0ba3a6542bb7e;hb=d01453133dd3b6247e4d0a12a6dd6886d6053a6c;hp=10ae253b519705857efbdb7e54217d2602285339;hpb=dad3f91c2f9a38ce8c64a688b6f1ba4f539af9fc;p=jalview.git
diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 10ae253..892b1b1 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -193,16 +193,14 @@ public class AAFrequency
* The alignment column on which the first profile is based.
* @param end
* The alignment column on which the last profile is based.
- * @param saveFullProfile
- * Flag for saving the counts for each profile
* @param removeBelowBackground
- * Flag for removing any characters with a match emission probability
- * less than its background frequency
+ * if true, symbols with a match emission probability less than
+ * background frequency are ignored
* @return
*/
public static ProfilesI calculateHMMProfiles(final HiddenMarkovModel hmm,
- int width, int start, int end, boolean saveFullProfile,
- boolean removeBelowBackground, boolean infoLetterHeight)
+ int width, int start, int end, boolean removeBelowBackground,
+ boolean infoLetterHeight)
{
ProfileI[] result = new ProfileI[width];
char[] symbols = hmm.getSymbols().toCharArray();
@@ -221,11 +219,7 @@ public class AAFrequency
int gapCount = counts.getGapCount();
ProfileI profile = new Profile(symbolCount, gapCount, maxCount,
maxResidue);
-
- if (saveFullProfile)
- {
- profile.setCounts(counts);
- }
+ profile.setCounts(counts);
result[column] = profile;
}
@@ -344,20 +338,16 @@ public class AAFrequency
* @param endCol
* end column (exclusive)
* @param ignoreGaps
- * if true, normalise residue percentages
+ * if true, normalise residue percentages
* @param showSequenceLogo
* if true include all information symbols, else just show modal
* residue
- * @param nseq
- * number of sequences
*/
public static float completeInformation(AlignmentAnnotation information,
- ProfilesI profiles, int startCol, int endCol, long nseq,
- Float currentMax)
+ ProfilesI profiles, int startCol, int endCol)
{
// long now = System.currentTimeMillis();
- if (information == null || information.annotations == null
- || information.annotations.length < endCol)
+ if (information == null || information.annotations == null)
{
/*
* called with a bad alignment annotation row
@@ -366,54 +356,48 @@ public class AAFrequency
return 0;
}
- Float max = 0f;
+ float max = 0f;
+ SequenceI hmmSeq = information.sequenceRef;
- for (int i = startCol; i < endCol; i++)
+ int seqLength = hmmSeq.getLength();
+ if (information.annotations.length < seqLength)
{
- ProfileI profile = profiles.get(i);
- if (profile == null)
+ return 0;
+ }
+
+ HiddenMarkovModel hmm = hmmSeq.getHMM();
+
+ for (int column = startCol; column < endCol; column++)
+ {
+ if (column >= seqLength)
{
- /*
- * happens if sequences calculated over were
- * shorter than alignment width
- */
- information.annotations[i] = null;
- return 0;
+ // hmm consensus sequence is shorter than the alignment
+ break;
}
- SequenceI hmmSeq = information.sequenceRef;
-
- HiddenMarkovModel hmm = hmmSeq.getHMM();
-
- float value = hmm.getInformationContent(i);
-
- if (value > max)
+ float value = hmm.getInformationContent(column);
+ boolean isNaN = Float.isNaN(value);
+ if (!isNaN)
{
- max = value;
+ max = Math.max(max, value);
}
- String description = value + " bits";
- information.annotations[i] = new Annotation(
- Character.toString(Character
- .toUpperCase(hmm.getConsensusAtAlignColumn(i))),
+ String description = isNaN ? null
+ : String.format("%.4f bits", value);
+ information.annotations[column] = new Annotation(
+ Character.toString(
+ Character.toUpperCase(hmmSeq.getCharAt(column))),
description, ' ', value);
}
- if (max > currentMax)
- {
- information.graphMax = max;
- return max;
- }
- else
- {
- information.graphMax = currentMax;
- return currentMax;
- }
+
+ information.graphMax = max;
+ return max;
}
/**
- * Derive the gap count annotation row.
+ * Derive the occupancy count annotation
*
- * @param gaprow
+ * @param occupancy
* the annotation row to add annotations to
* @param profiles
* the source consensus data
@@ -422,11 +406,11 @@ public class AAFrequency
* @param endCol
* end column (exclusive)
*/
- public static void completeGapAnnot(AlignmentAnnotation gaprow,
+ public static void completeGapAnnot(AlignmentAnnotation occupancy,
ProfilesI profiles, int startCol, int endCol, long nseq)
{
- if (gaprow == null || gaprow.annotations == null
- || gaprow.annotations.length < endCol)
+ if (occupancy == null || occupancy.annotations == null
+ || occupancy.annotations.length < endCol)
{
/*
* called with a bad alignment annotation row
@@ -435,8 +419,8 @@ public class AAFrequency
return;
}
// always set ranges again
- gaprow.graphMax = nseq;
- gaprow.graphMin = 0;
+ occupancy.graphMax = nseq;
+ occupancy.graphMin = 0;
double scale = 0.8 / nseq;
for (int i = startCol; i < endCol; i++)
{
@@ -447,7 +431,7 @@ public class AAFrequency
* happens if sequences calculated over were
* shorter than alignment width
*/
- gaprow.annotations[i] = null;
+ occupancy.annotations[i] = null;
return;
}
@@ -455,7 +439,8 @@ public class AAFrequency
String description = "" + gapped;
- gaprow.annotations[i] = new Annotation("", description, '\0', gapped,
+ occupancy.annotations[i] = new Annotation("", description, '\0',
+ gapped,
jalview.util.ColorUtils.bleachColour(Color.DARK_GRAY,
(float) scale * gapped));
}
@@ -520,7 +505,7 @@ public class AAFrequency
* contains
*
*
- * [profileType, numberOfValues, nonGapCount, charValue1, percentage1, charValue2, percentage2, ...]
+ * [profileType, numberOfValues, totalPercent, charValue1, percentage1, charValue2, percentage2, ...]
* in descending order of percentage value
*
*
@@ -533,7 +518,6 @@ public class AAFrequency
*/
public static int[] extractProfile(ProfileI profile, boolean ignoreGaps)
{
- int[] rtnval = new int[64];
ResidueCount counts = profile.getCounts();
if (counts == null)
{
@@ -544,7 +528,6 @@ public class AAFrequency
char[] symbols = symbolCounts.symbols;
int[] values = symbolCounts.values;
QuickSort.sort(values, symbols);
- int nextArrayPos = 2;
int totalPercentage = 0;
final int divisor = ignoreGaps ? profile.getNonGapped()
: profile.getHeight();
@@ -552,21 +535,44 @@ public class AAFrequency
/*
* traverse the arrays in reverse order (highest counts first)
*/
+ int[] result = new int[3 + 2 * symbols.length];
+ int nextArrayPos = 3;
+ int nonZeroCount = 0;
+
for (int i = symbols.length - 1; i >= 0; i--)
{
int theChar = symbols[i];
int charCount = values[i];
-
- rtnval[nextArrayPos++] = theChar;
final int percentage = (charCount * 100) / divisor;
- rtnval[nextArrayPos++] = percentage;
+ if (percentage == 0)
+ {
+ /*
+ * this count (and any remaining) round down to 0% - discard
+ */
+ break;
+ }
+ nonZeroCount++;
+ result[nextArrayPos++] = theChar;
+ result[nextArrayPos++] = percentage;
totalPercentage += percentage;
}
- rtnval[0] = symbols.length;
- rtnval[1] = totalPercentage;
- int[] result = new int[rtnval.length + 1];
+
+ /*
+ * truncate array if any zero values were discarded
+ */
+ if (nonZeroCount < symbols.length)
+ {
+ int[] tmp = new int[3 + 2 * nonZeroCount];
+ System.arraycopy(result, 0, tmp, 0, tmp.length);
+ result = tmp;
+ }
+
+ /*
+ * fill in 'header' values
+ */
result[0] = AlignmentAnnotation.SEQUENCE_PROFILE;
- System.arraycopy(rtnval, 0, result, 1, rtnval.length);
+ result[1] = nonZeroCount;
+ result[2] = totalPercentage;
return result;
}
@@ -577,15 +583,15 @@ public class AAFrequency
* contains
*
*
- * [profileType, numberOfValues, totalCount, charValue1, percentage1, charValue2, percentage2, ...]
+ * [profileType, numberOfValues, totalPercentage, charValue1, percentage1, charValue2, percentage2, ...]
* in descending order of percentage value, where the character values encode codon triplets
*
*
* @param hashtable
* @return
*/
- public static int[] extractCdnaProfile(Hashtable hashtable,
- boolean ignoreGaps)
+ public static int[] extractCdnaProfile(
+ Hashtable hashtable, boolean ignoreGaps)
{
// this holds #seqs, #ungapped, and then codon count, indexed by encoded
// codon triplet
@@ -615,9 +621,16 @@ public class AAFrequency
{
break; // nothing else of interest here
}
+ final int percentage = codonCount * 100 / divisor;
+ if (percentage == 0)
+ {
+ /*
+ * this (and any remaining) values rounded down to 0 - discard
+ */
+ break;
+ }
distinctValuesCount++;
result[j++] = codons[i];
- final int percentage = codonCount * 100 / divisor;
result[j++] = percentage;
totalPercentage += percentage;
}
@@ -641,7 +654,7 @@ public class AAFrequency
* the consensus data stores to be populated (one per column)
*/
public static void calculateCdna(AlignmentI alignment,
- Hashtable[] hconsensus)
+ Hashtable[] hconsensus)
{
final char gapCharacter = alignment.getGapCharacter();
List mappings = alignment.getCodonFrames();
@@ -654,7 +667,7 @@ public class AAFrequency
for (int col = 0; col < cols; col++)
{
// todo would prefer a Java bean for consensus data
- Hashtable columnHash = new Hashtable<>();
+ Hashtable columnHash = new Hashtable<>();
// #seqs, #ungapped seqs, counts indexed by (codon encoded + 1)
int[] codonCounts = new int[66];
codonCounts[0] = alignment.getSequences().size();
@@ -674,6 +687,7 @@ public class AAFrequency
{
codonCounts[codonEncoded + 2]++;
ungappedCount++;
+ break;
}
}
}
@@ -699,7 +713,8 @@ public class AAFrequency
*/
public static void completeCdnaConsensus(
AlignmentAnnotation consensusAnnotation,
- Hashtable[] consensusData, boolean showProfileLogo, int nseqs)
+ Hashtable[] consensusData,
+ boolean showProfileLogo, int nseqs)
{
if (consensusAnnotation == null
|| consensusAnnotation.annotations == null
@@ -714,7 +729,7 @@ public class AAFrequency
consensusAnnotation.scaleColLabel = true;
for (int col = 0; col < consensusData.length; col++)
{
- Hashtable hci = consensusData[col];
+ Hashtable hci = consensusData[col];
if (hci == null)
{
// gapped protein column?