X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=0ea479dd07671da35efe3dc112d86f8ad3754e0f;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=bb554262f5674bcedb5382c9b978602e7077d93c;hpb=a4a68a8b10217312efe5f2ea4746f1cfc9da155d;p=jalview.git
diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index bb55426..0ea479d 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -1,20 +1,19 @@
/*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
*/
package jalview.analysis;
@@ -40,6 +39,10 @@ import jalview.util.*;
*/
public class AlignmentSorter
{
+ /**
+ * todo: refactor searches to follow a basic pattern: (search property, last
+ * search state, current sort direction)
+ */
static boolean sortIdAscending = true;
static int lastGroupHash = 0;
@@ -59,42 +62,48 @@ public class AlignmentSorter
*/
private static String lastSortByScore;
+ private static boolean sortByScoreAscending = true;
+
/**
* compact representation of last arguments to SortByFeatureScore
*/
private static String lastSortByFeatureScore;
+ private static boolean sortByFeatureScoreAscending = true;
+
private static boolean sortLengthAscending;
/**
* Sort by Percentage Identity w.r.t. s
*
* @param align
- * AlignmentI
+ * AlignmentI
* @param s
- * SequenceI
+ * SequenceI
* @param tosort
- * sequences from align that are to be sorted.
+ * sequences from align that are to be sorted.
*/
public static void sortByPID(AlignmentI align, SequenceI s,
SequenceI[] tosort)
{
- sortByPID(align,s,tosort,0,-1);
+ sortByPID(align, s, tosort, 0, -1);
}
+
/**
* Sort by Percentage Identity w.r.t. s
*
* @param align
- * AlignmentI
+ * AlignmentI
* @param s
- * SequenceI
+ * SequenceI
* @param tosort
- * sequences from align that are to be sorted.
- * @param start start column (0 for beginning
+ * 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)
+ SequenceI[] tosort, int start, int end)
{
int nSeq = align.getHeight();
@@ -117,9 +126,9 @@ public class AlignmentSorter
* Reverse the order of the sort
*
* @param align
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param seqs
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
private static void setReverseOrder(AlignmentI align, SequenceI[] seqs)
{
@@ -149,9 +158,9 @@ public class AlignmentSorter
* Sets the Alignment object with the given sequences
*
* @param align
- * Alignment object to be updated
+ * Alignment object to be updated
* @param tmp
- * sequences as a vector
+ * sequences as a vector
*/
private static void setOrder(AlignmentI align, Vector tmp)
{
@@ -162,9 +171,9 @@ public class AlignmentSorter
* Sets the Alignment object with the given sequences
*
* @param align
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param seqs
- * sequences as an array
+ * sequences as an array
*/
public static void setOrder(AlignmentI align, SequenceI[] seqs)
{
@@ -193,7 +202,7 @@ public class AlignmentSorter
* Sorts by ID. Numbers are sorted before letters.
*
* @param align
- * The alignment object to sort
+ * The alignment object to sort
*/
public static void sortByID(AlignmentI align)
{
@@ -221,11 +230,12 @@ public class AlignmentSorter
sortIdAscending = !sortIdAscending;
}
+
/**
* Sorts by sequence length
*
* @param align
- * The alignment object to sort
+ * The alignment object to sort
*/
public static void sortByLength(AlignmentI align)
{
@@ -233,11 +243,11 @@ public class AlignmentSorter
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());
+ length[i] = (float) (seqs[i].getEnd() - seqs[i].getStart());
}
QuickSort.sort(length, seqs);
@@ -260,7 +270,7 @@ public class AlignmentSorter
* object.
*
* @param align
- * sorts the given alignment object by group
+ * sorts the given alignment object by group
*/
public static void sortByGroup(AlignmentI align)
{
@@ -332,7 +342,7 @@ public class AlignmentSorter
* Converts Vector to array. java 1.18 does not have Vector.toArray()
*
* @param tmp
- * Vector of SequenceI objects
+ * Vector of SequenceI objects
*
* @return array of Sequence[]
*/
@@ -352,16 +362,16 @@ public class AlignmentSorter
* DOCUMENT ME!
*
* @param tmp
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param mask
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
private static SequenceI[] vectorSubsetToArray(Vector tmp, Vector mask)
{
Vector seqs = new Vector();
- int i;
+ int i, idx;
boolean[] tmask = new boolean[mask.size()];
for (i = 0; i < mask.size(); i++)
@@ -372,10 +382,10 @@ public class AlignmentSorter
for (i = 0; i < tmp.size(); i++)
{
Object sq = tmp.elementAt(i);
-
- if (mask.contains(sq) && tmask[mask.indexOf(sq)])
+ idx = mask.indexOf(sq);
+ if (idx > -1 && tmask[idx])
{
- tmask[mask.indexOf(sq)] = false;
+ tmask[idx] = false;
seqs.addElement(sq);
}
}
@@ -395,9 +405,9 @@ public class AlignmentSorter
* Sorts by a given AlignmentOrder object
*
* @param align
- * Alignment to order
+ * Alignment to order
* @param order
- * specified order for alignment
+ * specified order for alignment
*/
public static void sortBy(AlignmentI align, AlignmentOrder order)
{
@@ -427,9 +437,9 @@ public class AlignmentSorter
* DOCUMENT ME!
*
* @param align
- * alignment to order
+ * alignment to order
* @param tree
- * tree which has
+ * tree which has
*
* @return DOCUMENT ME!
*/
@@ -465,9 +475,9 @@ public class AlignmentSorter
* Sorts the alignment by a given tree
*
* @param align
- * alignment to order
+ * alignment to order
* @param tree
- * tree which has
+ * tree which has
*/
public static void sortByTree(AlignmentI align, NJTree tree)
{
@@ -498,9 +508,9 @@ public class AlignmentSorter
* DOCUMENT ME!
*
* @param align
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param seqs
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
private static void addStrays(AlignmentI align, Vector seqs)
{
@@ -525,11 +535,11 @@ public class AlignmentSorter
* DOCUMENT ME!
*
* @param node
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param tmp
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param seqset
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
@@ -595,17 +605,17 @@ public class AlignmentSorter
* particular scoreLabel. Or reverse if same label was used previously
*
* @param scoreLabel
- * exact label for sequence associated AlignmentAnnotation
- * scores to use for sorting.
+ * exact label for sequence associated AlignmentAnnotation scores to
+ * use for sorting.
* @param alignment
- * sequences to be sorted
+ * sequences to be sorted
*/
public static void sortByAnnotationScore(String scoreLabel,
AlignmentI alignment)
{
SequenceI[] seqs = alignment.getSequencesArray();
boolean[] hasScore = new boolean[seqs.length]; // per sequence score
- // presence
+ // presence
int hasScores = 0; // number of scores present on set
double[] scores = new double[seqs.length];
double min = 0, max = 0;
@@ -617,7 +627,7 @@ public class AlignmentSorter
hasScores++;
hasScore[i] = true;
scores[i] = scoreAnn[0].getScore(); // take the first instance of this
- // score.
+ // score.
if (hasScores == 1)
{
max = min = scores[i];
@@ -649,7 +659,7 @@ public class AlignmentSorter
{
if (!hasScore[i])
{
- scores[i] = (max + i+1.0);
+ scores[i] = (max + i + 1.0);
}
}
}
@@ -665,73 +675,94 @@ 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
+ * 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";
-
+ 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
+ * 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)
+ 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);
+ 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)
+
+ private static boolean containsIgnoreCase(final String lab,
+ final String[] labs)
{
- if (labs==null)
+ if (labs == null)
{
return true;
}
- if (lab==null)
+ 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))
+ (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))))
+ // 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 {
+ }
+ else
+ {
// or, also take a look at the scores if necessary.
- if (!ignoreScore && sf[f].getScore()!=Float.NaN)
+ if (!ignoreScore && sf[f].getScore() != Float.NaN)
{
- if (seqScores[i]==0)
+ if (seqScores[i] == 0)
{
hasScores++;
}
seqScores[i]++;
hasScore[i] = true;
scores[i] += sf[f].getScore(); // take the first instance of this
- // score.
+ // score.
}
}
}
SequenceFeature[] fs;
feats[i] = fs = new SequenceFeature[n];
- if (n>0)
+ if (n > 0)
{
- n=0;
- for (int f=0;f