X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=2fad332458ff5f63f5a3f7d4bdc3b28a180e6006;hb=1ae9824ef37ce4ed36d1da986003474b47d1ab11;hp=881dc74b8020887d88325b805dfe58b7f0204b56;hpb=f52f7b378972cc884b5d3e5cc250f89667f558f7;p=jalview.git
diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 881dc74..2fad332 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -1,26 +1,38 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
* This file is part of Jalview.
- *
+ *
* 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.
- *
- * 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
+ * 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.
+ *
+ * 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 .
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
-import java.util.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentOrder;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequenceNode;
+import jalview.util.Comparison;
+import jalview.util.MessageManager;
+import jalview.util.QuickSort;
-import jalview.datamodel.*;
-import jalview.util.*;
+import java.util.ArrayList;
+import java.util.List;
/**
* Routines for manipulating the order of a multiple sequence alignment TODO:
@@ -75,7 +87,7 @@ public class AlignmentSorter
/**
* Sort by Percentage Identity w.r.t. s
- *
+ *
* @param align
* AlignmentI
* @param s
@@ -91,7 +103,7 @@ public class AlignmentSorter
/**
* Sort by Percentage Identity w.r.t. s
- *
+ *
* @param align
* AlignmentI
* @param s
@@ -117,14 +129,14 @@ public class AlignmentSorter
seqs[i] = align.getSequenceAt(i);
}
- QuickSort.sort(scores, 0, scores.length - 1, seqs);
+ QuickSort.sort(scores, seqs);
setReverseOrder(align, seqs);
}
/**
* Reverse the order of the sort
- *
+ *
* @param align
* DOCUMENT ME!
* @param seqs
@@ -160,20 +172,20 @@ public class AlignmentSorter
/**
* Sets the Alignment object with the given sequences
- *
+ *
* @param align
* Alignment object to be updated
* @param tmp
* sequences as a vector
*/
- private static void setOrder(AlignmentI align, Vector tmp)
+ private static void setOrder(AlignmentI align, List tmp)
{
setOrder(align, vectorSubsetToArray(tmp, align.getSequences()));
}
/**
* Sets the Alignment object with the given sequences
- *
+ *
* @param align
* DOCUMENT ME!
* @param seqs
@@ -206,7 +218,7 @@ public class AlignmentSorter
/**
* Sorts by ID. Numbers are sorted before letters.
- *
+ *
* @param align
* The alignment object to sort
*/
@@ -239,7 +251,7 @@ public class AlignmentSorter
/**
* Sorts by sequence length
- *
+ *
* @param align
* The alignment object to sort
*/
@@ -274,7 +286,7 @@ public class AlignmentSorter
* Sorts the alignment by size of group.
* Maintains the order of sequences in each group by order in given alignment
* object.
- *
+ *
* @param align
* sorts the given alignment object by group
*/
@@ -282,7 +294,7 @@ public class AlignmentSorter
{
// MAINTAINS ORIGNAL SEQUENCE ORDER,
// ORDERS BY GROUP SIZE
- Vector groups = new Vector();
+ List groups = new ArrayList();
if (groups.hashCode() != lastGroupHash)
{
@@ -300,11 +312,11 @@ public class AlignmentSorter
{
for (int j = 0; j < groups.size(); j++)
{
- SequenceGroup sg2 = (SequenceGroup) groups.elementAt(j);
+ SequenceGroup sg2 = groups.get(j);
if (sg.getSize() > sg2.getSize())
{
- groups.insertElementAt(sg, j);
+ groups.add(j, sg);
break;
}
@@ -312,22 +324,22 @@ public class AlignmentSorter
if (!groups.contains(sg))
{
- groups.addElement(sg);
+ groups.add(sg);
}
}
// NOW ADD SEQUENCES MAINTAINING ALIGNMENT ORDER
// /////////////////////////////////////////////
- Vector seqs = new Vector();
+ List seqs = new ArrayList();
for (int i = 0; i < groups.size(); i++)
{
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+ SequenceGroup sg = groups.get(i);
SequenceI[] orderedseqs = sg.getSequencesInOrder(align);
for (int j = 0; j < orderedseqs.length; j++)
{
- seqs.addElement(orderedseqs[j]);
+ seqs.add(orderedseqs[j]);
}
}
@@ -343,39 +355,23 @@ public class AlignmentSorter
}
/**
- * Converts Vector to array. java 1.18 does not have Vector.toArray()
- *
- * @param tmp
- * Vector of SequenceI objects
- *
- * @return array of Sequence[]
- */
- private static SequenceI[] vectorToArray(Vector tmp)
- {
- SequenceI[] seqs = new SequenceI[tmp.size()];
-
- for (int i = 0; i < tmp.size(); i++)
- {
- seqs[i] = (SequenceI) tmp.elementAt(i);
- }
-
- return seqs;
- }
-
- /**
* Select sequences in order from tmp that is present in mask, and any
- * remaining seqeunces in mask not in tmp
- *
+ * remaining sequences in mask not in tmp
+ *
* @param tmp
* thread safe collection of sequences
* @param mask
* thread safe collection of sequences
- *
+ *
* @return intersect(tmp,mask)+intersect(complement(tmp),mask)
*/
private static SequenceI[] vectorSubsetToArray(List tmp,
List mask)
{
+ // or?
+ // tmp2 = tmp.retainAll(mask);
+ // return tmp2.addAll(mask.removeAll(tmp2))
+
ArrayList seqs = new ArrayList();
int i, idx;
boolean[] tmask = new boolean[mask.size()];
@@ -409,7 +405,7 @@ public class AlignmentSorter
/**
* Sorts by a given AlignmentOrder object
- *
+ *
* @param align
* Alignment to order
* @param order
@@ -418,7 +414,7 @@ public class AlignmentSorter
public static void sortBy(AlignmentI align, AlignmentOrder order)
{
// Get an ordered vector of sequences which may also be present in align
- Vector tmp = order.getOrder();
+ List tmp = order.getOrder();
if (lastOrder == order)
{
@@ -441,19 +437,20 @@ public class AlignmentSorter
/**
* DOCUMENT ME!
- *
+ *
* @param align
* alignment to order
* @param tree
* tree which has
- *
+ *
* @return DOCUMENT ME!
*/
- private static Vector getOrderByTree(AlignmentI align, NJTree tree)
+ private static List getOrderByTree(AlignmentI align,
+ NJTree tree)
{
int nSeq = align.getHeight();
- Vector tmp = new Vector();
+ List tmp = new ArrayList();
tmp = _sortByTree(tree.getTopNode(), tmp, align.getSequences());
@@ -483,7 +480,7 @@ public class AlignmentSorter
/**
* Sorts the alignment by a given tree
- *
+ *
* @param align
* alignment to order
* @param tree
@@ -491,7 +488,7 @@ public class AlignmentSorter
*/
public static void sortByTree(AlignmentI align, NJTree tree)
{
- Vector tmp = getOrderByTree(align, tree);
+ List tmp = getOrderByTree(align, tree);
// tmp should properly permute align with tree.
if (lastTree != tree)
@@ -516,25 +513,25 @@ public class AlignmentSorter
/**
* DOCUMENT ME!
- *
+ *
* @param align
* DOCUMENT ME!
- * @param seqs
+ * @param tmp
* DOCUMENT ME!
*/
- private static void addStrays(AlignmentI align, Vector seqs)
+ private static void addStrays(AlignmentI align, List tmp)
{
int nSeq = align.getHeight();
for (int i = 0; i < nSeq; i++)
{
- if (!seqs.contains(align.getSequenceAt(i)))
+ if (!tmp.contains(align.getSequenceAt(i)))
{
- seqs.addElement(align.getSequenceAt(i));
+ tmp.add(align.getSequenceAt(i));
}
}
- if (nSeq != seqs.size())
+ if (nSeq != tmp.size())
{
System.err
.println("ERROR: Size still not right even after addStrays");
@@ -543,17 +540,18 @@ public class AlignmentSorter
/**
* DOCUMENT ME!
- *
+ *
* @param node
* DOCUMENT ME!
* @param tmp
* DOCUMENT ME!
* @param seqset
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
- private static Vector _sortByTree(SequenceNode node, Vector tmp,
+ private static List _sortByTree(SequenceNode node,
+ List tmp,
List seqset)
{
if (node == null)
@@ -574,7 +572,7 @@ public class AlignmentSorter
// seqset.size()==0 ||
// seqset.contains(tmp)))
{
- tmp.addElement(node.element());
+ tmp.add((SequenceI) node.element());
}
}
}
@@ -615,7 +613,7 @@ public class AlignmentSorter
/**
* Sort sequence in order of increasing score attribute for annotation with a
* particular scoreLabel. Or reverse if same label was used previously
- *
+ *
* @param scoreLabel
* exact label for sequence associated AlignmentAnnotation scores to
* use for sorting.
@@ -703,7 +701,7 @@ public class AlignmentSorter
/**
* 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
@@ -754,8 +752,7 @@ public class AlignmentSorter
if (method != FEATURE_SCORE && method != FEATURE_LABEL
&& method != FEATURE_DENSITY)
{
- throw new Error(
- "Implementation Error - sortByFeature method must be one of FEATURE_SCORE, FEATURE_LABEL or FEATURE_DENSITY.");
+ throw new Error(MessageManager.getString("error.implementation_error_sortbyfeature"));
}
boolean ignoreScore = method != FEATURE_SCORE;
StringBuffer scoreLabel = new StringBuffer();
@@ -783,10 +780,6 @@ public class AlignmentSorter
for (int i = 0; i < seqs.length; i++)
{
SequenceFeature[] sf = seqs[i].getSequenceFeatures();
- if (sf == null && seqs[i].getDatasetSequence() != null)
- {
- sf = seqs[i].getDatasetSequence().getSequenceFeatures();
- }
if (sf == null)
{
sf = new SequenceFeature[0];
@@ -935,7 +928,7 @@ public class AlignmentSorter
{
if (method == FEATURE_LABEL)
{
- throw new Error("Not yet implemented.");
+ throw new Error(MessageManager.getString("error.not_yet_implemented"));
}
}
if (lastSortByFeatureScore == null