X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAAFrequency.java;h=b1505d6827ce8401af83960a821cc6d4b3a1a5ea;hb=a6f0678764ea06034460236c7a811bbfcad682aa;hp=ee16f9455665b7c698c84664941896ad2d1e8473;hpb=aaa5a9341963ac324baa558bf3f5b744cfdee9c7;p=jalview.git diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java index ee16f94..b1505d6 100755 --- a/src/jalview/analysis/AAFrequency.java +++ b/src/jalview/analysis/AAFrequency.java @@ -20,10 +20,6 @@ */ package jalview.analysis; -import java.util.Arrays; -import java.util.Hashtable; -import java.util.List; - import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; @@ -41,6 +37,11 @@ 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; + /** * Takes in a vector or array of sequences and column start and column end and * returns a new Hashtable[] of size maxSeqLength, if Hashtable not supplied. @@ -146,14 +147,13 @@ public class AAFrequency { if (sequences[row] == null) { - System.err - .println("WARNING: Consensus skipping null sequence - possible race condition."); + System.err.println( + "WARNING: Consensus skipping null sequence - possible race condition."); continue; } - char[] seq = sequences[row].getSequence(); - if (seq.length > column) + if (sequences[row].getLength() > column) { - char c = seq[column]; + char c = sequences[row].getCharAt(column); residueCounts.add(c); if (Comparison.isNucleotide(c)) { @@ -315,6 +315,7 @@ public class AAFrequency // 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); @@ -330,11 +331,11 @@ public class AAFrequency final int gapped = profile.getNonGapped(); - String description = String.valueOf(gapped); + String description = "" + gapped; - gaprow.annotations[i] = new Annotation(description, description, - '\0', - gapped); + gaprow.annotations[i] = new Annotation("", description, '\0', gapped, + jalview.util.ColorUtils.bleachColour(Color.DARK_GRAY, + (float) scale * gapped)); } } @@ -343,7 +344,8 @@ public class AAFrequency *
- * [profileType, numberOfValues, nonGapCount, charValue1, percentage1, charValue2, percentage2, ...] + * [profileType, numberOfValues, totalPercent, charValue1, percentage1, charValue2, percentage2, ...] * in descending order of percentage value ** @@ -409,7 +411,6 @@ public class AAFrequency */ public static int[] extractProfile(ProfileI profile, boolean ignoreGaps) { - int[] rtnval = new int[64]; ResidueCount counts = profile.getCounts(); if (counts == null) { @@ -420,29 +421,51 @@ 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(); + final int divisor = ignoreGaps ? profile.getNonGapped() + : profile.getHeight(); /* * 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; } @@ -452,15 +475,15 @@ 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