X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=bb554262f5674bcedb5382c9b978602e7077d93c;hb=50ae21686bb576ce02f2a83a1d53744b86290479;hp=fe2cfc7c7dfb70d5861f72c2dbc52831a3e3c743;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git
diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index fe2cfc7..bb55426 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -1,6 +1,6 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
@@ -54,9 +54,19 @@ public class AlignmentSorter
static boolean sortTreeAscending = true;
+ /**
+ * last Annotation Label used by sortByScore
+ */
private static String lastSortByScore;
/**
+ * compact representation of last arguments to SortByFeatureScore
+ */
+ private static String lastSortByFeatureScore;
+
+ private static boolean sortLengthAscending;
+
+ /**
* Sort by Percentage Identity w.r.t. s
*
* @param align
@@ -69,6 +79,23 @@ public class AlignmentSorter
public static void sortByPID(AlignmentI align, SequenceI s,
SequenceI[] tosort)
{
+ sortByPID(align,s,tosort,0,-1);
+ }
+ /**
+ * Sort by Percentage Identity w.r.t. s
+ *
+ * @param align
+ * AlignmentI
+ * @param s
+ * SequenceI
+ * @param tosort
+ * sequences from align that are to be sorted.
+ * @param start start column (0 for beginning
+ * @param end
+ */
+ public static void sortByPID(AlignmentI align, SequenceI s,
+ SequenceI[] tosort,int start, int end)
+ {
int nSeq = align.getHeight();
float[] scores = new float[nSeq];
@@ -194,6 +221,38 @@ public class AlignmentSorter
sortIdAscending = !sortIdAscending;
}
+ /**
+ * Sorts by sequence length
+ *
+ * @param align
+ * The alignment object to sort
+ */
+ public static void sortByLength(AlignmentI align)
+ {
+ int nSeq = align.getHeight();
+
+ float[] length = new float[nSeq];
+ SequenceI[] seqs = new SequenceI[nSeq];
+
+ for (int i = 0; i < nSeq; i++)
+ {
+ seqs[i] = align.getSequenceAt(i);
+ length[i] = (float) (seqs[i].getEnd()-seqs[i].getStart());
+ }
+
+ QuickSort.sort(length, seqs);
+
+ if (sortLengthAscending)
+ {
+ setReverseOrder(align, seqs);
+ }
+ else
+ {
+ setOrder(align, seqs);
+ }
+
+ sortLengthAscending = !sortLengthAscending;
+ }
/**
* Sorts the alignment by size of group.
@@ -590,7 +649,7 @@ public class AlignmentSorter
{
if (!hasScore[i])
{
- scores[i] = (max + i);
+ scores[i] = (max + i+1.0);
}
}
}
@@ -606,4 +665,231 @@ public class AlignmentSorter
setReverseOrder(alignment, seqs);
}
}
+ /**
+ * types of feature ordering:
+ * Sort by score : average score - or total score - over all features in region
+ * Sort by feature label text: (or if null - feature type text) - numerical or alphabetical
+ * Sort by feature density: based on counts - ignoring individual text or scores for each feature
+ */
+ public static String FEATURE_SCORE="average_score";
+ public static String FEATURE_LABEL="text";
+ public static String FEATURE_DENSITY="density";
+
+ /**
+ * sort the alignment using the features on each sequence found between start and stop with the given featureLabel (and optional group qualifier)
+ * @param featureLabel (may not be null)
+ * @param groupLabel (may be null)
+ * @param start (-1 to include non-positional features)
+ * @param stop (-1 to only sort on non-positional features)
+ * @param alignment - aligned sequences containing features
+ * @param method - one of the string constants FEATURE_SCORE, FEATURE_LABEL, FEATURE_DENSITY
+ */
+ public static void sortByFeature(String featureLabel, String groupLabel, int start, int stop,
+ AlignmentI alignment, String method)
+ {
+ sortByFeature(featureLabel==null ? null : new String[] {featureLabel},
+ groupLabel==null ? null : new String[] {groupLabel}, start, stop, alignment, method);
+ }
+ private static boolean containsIgnoreCase(final String lab, final String[] labs)
+ {
+ if (labs==null)
+ {
+ return true;
+ }
+ if (lab==null)
+ {
+ return false;
+ }
+ for (int q=0;q sstop)
+ ||
+ // or ignore based on selection criteria
+ (featureLabels != null && !AlignmentSorter.containsIgnoreCase(sf[f].type, featureLabels))
+ || (groupLabels != null
+ // problem here: we cannot eliminate null feature group features
+ && (sf[f].getFeatureGroup() != null
+ && !AlignmentSorter.containsIgnoreCase(sf[f].getFeatureGroup(), groupLabels))))
+ {
+ // forget about this feature
+ sf[f] = null;
+ n--;
+ } else {
+ // or, also take a look at the scores if necessary.
+ if (!ignoreScore && sf[f].getScore()!=Float.NaN)
+ {
+ if (seqScores[i]==0)
+ {
+ hasScores++;
+ }
+ seqScores[i]++;
+ hasScore[i] = true;
+ scores[i] += sf[f].getScore(); // take the first instance of this
+ // score.
+ }
+ }
+ }
+ SequenceFeature[] fs;
+ feats[i] = fs = new SequenceFeature[n];
+ if (n>0)
+ {
+ n=0;
+ for (int f=0;f scores[i])
+ {
+ min = scores[i];
+ }
+ }
+ }
+ }
+
+ if (method==FEATURE_SCORE)
+ {
+ if (hasScores == 0)
+ {
+ return; // do nothing - no scores present to sort by.
+ }
+ // pad score matrix
+ if (hasScores < seqs.length)
+ {
+ for (int i = 0; i < seqs.length; i++)
+ {
+ if (!hasScore[i])
+ {
+ scores[i] = (max + i);
+ } else {
+ int nf=(feats[i]==null) ? 0 :((SequenceFeature[]) feats[i]).length;
+ System.err.println("Sorting on Score: seq "+seqs[i].getName()+ " Feats: "+nf+" Score : "+scores[i]);
+ }
+ }
+ }
+
+ jalview.util.QuickSort.sort(scores, seqs);
+ }
+ else
+ if (method==FEATURE_DENSITY)
+ {
+
+ // break ties between equivalent numbers for adjacent sequences by adding 1/Nseq*i on the original order
+ double fr = 0.9/(1.0*seqs.length);
+ for (int i=0;i