-package jalview.analysis;\r
-\r
-import jalview.datamodel.*;\r
-import jalview.util.*;\r
-import jalview.io.*;\r
-\r
-import java.util.*;\r
-\r
-/** Data structure to hold and manipulate a multiple sequence alignment\r
- */\r
-public class AlignmentSorter {\r
-\r
- private AlignmentSorter() {\r
- try\r
- {\r
- jbInit();\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
-\r
- public static void sortGroups(AlignmentI align) {\r
- Vector groups = align.getGroups();\r
- int nGroup = groups.size();\r
-\r
- float[] arr = new float [nGroup];\r
- Object[] s = new Object[nGroup];\r
-\r
- for (int i=0; i < nGroup; i++) {\r
- arr[i] = ((SequenceGroup)groups.elementAt(i)).getSize();\r
- s[i] = groups.elementAt(i);\r
- }\r
-\r
- QuickSort.sort(arr,s);\r
-\r
- Vector newg = new Vector(nGroup);\r
-\r
- for (int i=nGroup-1; i >= 0; i--) {\r
- newg.addElement(s[i]);\r
- }\r
-\r
- // align.setGroups(newg);\r
- }\r
-\r
- /**\r
- * Sort by Percentage Identity\r
- *\r
- * @param align AlignmentI\r
- * @param s SequenceI\r
- */\r
- public static void sortByPID(AlignmentI align, SequenceI s) {\r
- int nSeq = align.getHeight();\r
-\r
- float scores[] = new float[nSeq];\r
- SequenceI seqs[] = new SequenceI[nSeq];\r
-\r
- for (int i = 0; i < nSeq; i++) {\r
- scores[i] = Comparison.compare(align.getSequenceAt(i),s);\r
- seqs[i] = align.getSequenceAt(i);\r
- }\r
-\r
- QuickSort.sort(scores,0,scores.length-1,seqs);\r
-\r
- setReverseOrder(align,seqs);\r
- }\r
-\r
- private static void setReverseOrder(AlignmentI align, SequenceI [] seqs) {\r
- int nSeq = seqs.length;\r
-\r
- int len = 0;\r
- if (nSeq%2 == 0) {\r
- len = nSeq/2;\r
- } else {\r
- len = (nSeq+1)/2;\r
- }\r
-\r
-// NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work\r
- for (int i = 0; i < len; i++) {\r
- //SequenceI tmp = seqs[i];\r
- align.getSequences().setElementAt(seqs[nSeq-i-1],i);\r
- align.getSequences().setElementAt(seqs[i],nSeq-i-1);\r
- }\r
- }\r
-\r
- private static void setOrder(AlignmentI align, Vector tmp) {\r
- setOrder(align,vectorSubsetToArray(tmp, align.getSequences()));\r
- }\r
-\r
- private static void setOrder(AlignmentI align, SequenceI [] seqs) {\r
- // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work\r
-\r
- Vector algn = align.getSequences();\r
-\r
- for (int i = 0, p = 0; i < seqs.length; i++)\r
- algn.setElementAt(seqs[i], p++);\r
- }\r
- /** */\r
- static boolean sortIdAscending = true;\r
- public static void sortByID(AlignmentI align) {\r
- int nSeq = align.getHeight();\r
-\r
- String ids[] = new String[nSeq];\r
- SequenceI seqs[] = new SequenceI[nSeq];\r
-\r
- for (int i = 0; i < nSeq; i++) {\r
- ids[i] = align.getSequenceAt(i).getName();\r
- seqs[i] = align.getSequenceAt(i);\r
- }\r
-\r
- QuickSort.sort(ids,seqs);\r
-\r
- if(sortIdAscending)\r
- setReverseOrder(align,seqs);\r
- else\r
- setOrder(align, seqs);\r
-\r
- sortIdAscending = !sortIdAscending;\r
- }\r
- static int lastGroupHash = 0;\r
- static boolean sortGroupAscending = true;\r
-\r
- public static void sortByGroup(AlignmentI align) {\r
- int nSeq = align.getHeight();\r
- Vector groups = align.getGroups();\r
- if (groups.hashCode()!=lastGroupHash) {\r
- sortGroupAscending=true;\r
- lastGroupHash = groups.hashCode();\r
- } else\r
- sortGroupAscending = ! sortGroupAscending;\r
-\r
- Vector seqs = new Vector();\r
-\r
- for (int i=0; i < groups.size(); i++) {\r
- SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
-\r
- for (int j = 0; j < sg.getSize(); j++) {\r
- seqs.addElement(sg.getSequenceAt(j));\r
- }\r
- }\r
-\r
- // Deletions can happen so this check may fail\r
- /*\r
- if (seqs.size() != nSeq) {\r
- System.err.println("ERROR: tmp.size() != nseq in sortByGroups");\r
- if (seqs.size() < nSeq) {\r
- addStrays(align,seqs);\r
- }\r
- }\r
-*/\r
- if(sortGroupAscending)\r
- setOrder(align,seqs);\r
- else\r
- setReverseOrder( align, vectorSubsetToArray(seqs, align.getSequences()));\r
-\r
- }\r
-\r
- private static SequenceI [] vectorToArray(Vector tmp) {\r
- SequenceI[] seqs = new SequenceI[tmp.size()];\r
-\r
- for (int i=0; i < tmp.size(); i++) {\r
- seqs[i] = (SequenceI)tmp.elementAt(i);\r
- }\r
- return seqs;\r
- }\r
-\r
- private static SequenceI [] vectorSubsetToArray(Vector tmp, Vector mask) {\r
- Vector seqs = new Vector();\r
- int i,m, p;\r
- boolean[] tmask = new boolean[m=mask.size()];\r
- for (i=0; i<m; i++)\r
- tmask[i] = true;\r
- for (i=0; i < tmp.size(); i++) {\r
- Object sq;\r
- if (mask.contains(sq=tmp.elementAt(i))) {\r
- tmask[mask.indexOf(sq)] = false;\r
- seqs.addElement(sq);\r
- m--;\r
- }\r
- }\r
- for (i=0; i<tmask.length; i++)\r
- if (tmask[i])\r
- seqs.addElement(mask.elementAt(i));\r
- return vectorToArray(seqs);\r
- }\r
-\r
- static AlignmentOrder lastOrder = null;\r
- static boolean sortOrderAscending = true;\r
-\r
- public static void sortBy(AlignmentI align, AlignmentOrder order) {\r
- // Get an ordered vector of sequences which may also be present in align\r
- Vector tmp = order.getOrder();\r
-// if (tmp.size()<align.getHeight())\r
-// addStrays(align, tmp);\r
- if (lastOrder==order)\r
- sortOrderAscending=!sortOrderAscending;\r
- else\r
- sortOrderAscending=true;\r
-\r
- if (sortOrderAscending)\r
- setOrder(align, tmp);\r
- else\r
- setReverseOrder(align, vectorSubsetToArray(tmp, align.getSequences()));\r
- }\r
- static NJTree lastTree = null;\r
- static boolean sortTreeAscending = true;\r
-\r
- public static Vector getOrderByTree(AlignmentI align, NJTree tree) {\r
- int nSeq = align.getHeight();\r
-\r
- Vector tmp = new Vector();\r
-\r
- tmp = _sortByTree(tree.getTopNode(), tmp, align.getSequences());\r
-\r
- if (tmp.size() != nSeq)\r
- {\r
- // TODO: JBPNote - decide if this is always an error\r
- // (eg. not when a tree is associated to another alignment which has more\r
- // sequences)\r
-\r
- if (tmp.size() < nSeq)\r
- {\r
- addStrays(align, tmp);\r
- }\r
- if (tmp.size() != nSeq)\r
- System.err.println("ERROR: tmp.size()="+tmp.size()+" != nseq="+nSeq+" in getOrderByTree");\r
-\r
- }\r
- return tmp;\r
- }\r
-\r
- public static void sortByTree(AlignmentI align, NJTree tree) {\r
- Vector tmp = getOrderByTree(align, tree);\r
- // tmp should properly permute align with tree.\r
- if(lastTree!=tree) {\r
- sortTreeAscending = true;\r
- lastTree = tree;\r
- } else {\r
- sortTreeAscending = !sortTreeAscending;\r
- }\r
- if(sortTreeAscending)\r
- setOrder(align,tmp);\r
- else\r
- setReverseOrder(align, vectorSubsetToArray(tmp, align.getSequences()));\r
- }\r
-\r
- private static void addStrays(AlignmentI align, Vector seqs) {\r
- int nSeq = align.getHeight();\r
- for (int i=0;i<nSeq;i++) {\r
- if (!seqs.contains(align.getSequenceAt(i))) {\r
- seqs.addElement(align.getSequenceAt(i));\r
- }\r
- }\r
- if (nSeq != seqs.size()) {\r
- System.err.println("ERROR: Size still not right even after addStrays");\r
- }\r
- }\r
-\r
- public static Vector _sortByTree(SequenceNode node, Vector tmp, Vector seqset) {\r
- if (node == null) {return tmp;}\r
-\r
- SequenceNode left = (SequenceNode)node.left();\r
- SequenceNode right = (SequenceNode)node.right();\r
-\r
- if (left == null && right == null) {\r
- if (!node.isPlaceholder() && node.element()!=null)\r
- if (node.element() instanceof SequenceI)\r
- if (!tmp.contains(node.element()))\r
- tmp.addElement((SequenceI)node.element());\r
- return tmp;\r
-\r
- } else {\r
- _sortByTree(left,tmp, seqset);\r
- _sortByTree(right,tmp, seqset);\r
- }\r
- return tmp;\r
- }\r
- // Ordering Objects\r
- // Alignment.sortBy(OrderObj) - sequence of sequence pointer refs in appropriate order\r
- //\r
-\r
- /**\r
- * recover the order of sequences given by the safe numbering scheme introducd\r
- * SeqsetUtils.uniquify.\r
- */\r
- public static void recoverOrder(SequenceI[] alignment) {\r
- float[] ids = new float[alignment.length];\r
- for (int i=0; i<alignment.length; i++)\r
- ids[i] = (new Float(alignment[i].getName().substring(8))).floatValue();\r
- jalview.util.QuickSort.sort(ids, alignment);\r
- }\r
-\r
- private void jbInit()\r
- throws Exception\r
- {\r
- }\r
-\r
-}\r
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2006 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
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* 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.
+*
+* 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
+*/
+package jalview.analysis;
+
+import jalview.datamodel.*;
+
+import jalview.util.*;
+
+import java.util.*;
+
+
+/** Data structure to hold and manipulate a multiple sequence alignment
+ */
+public class AlignmentSorter
+{
+ static boolean sortIdAscending = true;
+ static int lastGroupHash = 0;
+ static boolean sortGroupAscending = true;
+ static AlignmentOrder lastOrder = null;
+ static boolean sortOrderAscending = true;
+ static NJTree lastTree = null;
+ static boolean sortTreeAscending = true;
+
+ /**
+ * Sort by Percentage Identity
+ *
+ * @param align AlignmentI
+ * @param s SequenceI
+ */
+ public static void sortByPID(AlignmentI align, SequenceI s)
+ {
+ int nSeq = align.getHeight();
+
+ float[] scores = new float[nSeq];
+ SequenceI[] seqs = new SequenceI[nSeq];
+
+ for (int i = 0; i < nSeq; i++)
+ {
+ scores[i] = Comparison.PID(align.getSequenceAt(i).getSequence(),
+ s.getSequence());
+ seqs[i] = align.getSequenceAt(i);
+ }
+
+ QuickSort.sort(scores, 0, scores.length - 1, seqs);
+
+ setReverseOrder(align, seqs);
+ }
+
+ /**
+ * Reverse the order of the sort
+ *
+ * @param align DOCUMENT ME!
+ * @param seqs DOCUMENT ME!
+ */
+ private static void setReverseOrder(AlignmentI align, SequenceI[] seqs)
+ {
+ int nSeq = seqs.length;
+
+ int len = 0;
+
+ if ((nSeq % 2) == 0)
+ {
+ len = nSeq / 2;
+ }
+ else
+ {
+ len = (nSeq + 1) / 2;
+ }
+
+ // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
+ for (int i = 0; i < len; i++)
+ {
+ //SequenceI tmp = seqs[i];
+ align.getSequences().setElementAt(seqs[nSeq - i - 1], i);
+ align.getSequences().setElementAt(seqs[i], nSeq - i - 1);
+ }
+ }
+
+ /**
+ * 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)
+ {
+ setOrder(align, vectorSubsetToArray(tmp, align.getSequences()));
+ }
+
+ /**
+ * Sets the Alignment object with the given sequences
+ *
+ * @param align DOCUMENT ME!
+ * @param seqs sequences as an array
+ */
+ private static void setOrder(AlignmentI align, SequenceI[] seqs)
+ {
+ // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
+ Vector algn = align.getSequences();
+
+ for (int i = 0; i < seqs.length; i++)
+ {
+ algn.setElementAt(seqs[i], i);
+ }
+ }
+
+ /**
+ * Sorts by ID. Numbers are sorted before letters.
+ *
+ * @param align The alignment object to sort
+ */
+ public static void sortByID(AlignmentI align)
+ {
+ int nSeq = align.getHeight();
+
+ String[] ids = new String[nSeq];
+ SequenceI[] seqs = new SequenceI[nSeq];
+
+ for (int i = 0; i < nSeq; i++)
+ {
+ ids[i] = align.getSequenceAt(i).getName();
+ seqs[i] = align.getSequenceAt(i);
+ }
+
+ QuickSort.sort(ids, seqs);
+
+ if (sortIdAscending)
+ {
+ setReverseOrder(align, seqs);
+ }
+ else
+ {
+ setOrder(align, seqs);
+ }
+
+ sortIdAscending = !sortIdAscending;
+ }
+
+ /**
+ * Sorts the alignment by size of group.
+ * <br>Maintains the order of sequences in each group
+ * by order in given alignment object.
+ *
+ * @param align sorts the given alignment object by group
+ */
+ public static void sortByGroup(AlignmentI align)
+ {
+ //MAINTAINS ORIGNAL SEQUENCE ORDER,
+ //ORDERS BY GROUP SIZE
+ Vector groups = new Vector();
+
+ if (groups.hashCode() != lastGroupHash)
+ {
+ sortGroupAscending = true;
+ lastGroupHash = groups.hashCode();
+ }
+ else
+ {
+ sortGroupAscending = !sortGroupAscending;
+ }
+
+ //SORTS GROUPS BY SIZE
+ //////////////////////
+ for (int i = 0; i < align.getGroups().size(); i++)
+ {
+ SequenceGroup sg = (SequenceGroup) align.getGroups().elementAt(i);
+
+ for (int j = 0; j < groups.size(); j++)
+ {
+ SequenceGroup sg2 = (SequenceGroup) groups.elementAt(j);
+
+ if (sg.getSize(false) > sg2.getSize(false))
+ {
+ groups.insertElementAt(sg, j);
+
+ break;
+ }
+ }
+
+ if (!groups.contains(sg))
+ {
+ groups.addElement(sg);
+ }
+ }
+
+ //NOW ADD SEQUENCES MAINTAINING ALIGNMENT ORDER
+ ///////////////////////////////////////////////
+ Vector seqs = new Vector();
+
+ for (int i = 0; i < groups.size(); i++)
+ {
+ SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+ SequenceI[] orderedseqs = sg.getSequencesInOrder(align);
+
+ for (int j = 0; j < orderedseqs.length; j++)
+ {
+ seqs.addElement(orderedseqs[j]);
+ }
+ }
+
+ if (sortGroupAscending)
+ {
+ setOrder(align, seqs);
+ }
+ else
+ {
+ setReverseOrder(align,
+ vectorSubsetToArray(seqs, align.getSequences()));
+ }
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param tmp DOCUMENT ME!
+ * @param mask DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ private static SequenceI[] vectorSubsetToArray(Vector tmp, Vector mask)
+ {
+ Vector seqs = new Vector();
+ int i;
+ boolean[] tmask = new boolean[mask.size()];
+
+ for (i = 0; i < mask.size(); i++)
+ tmask[i] = true;
+
+ for (i = 0; i < tmp.size(); i++)
+ {
+ Object sq = tmp.elementAt(i);
+
+ if (mask.contains(sq) && tmask[mask.indexOf(sq)])
+ {
+ tmask[mask.indexOf(sq)] = false;
+ seqs.addElement(sq);
+ }
+ }
+
+ for (i = 0; i < tmask.length; i++)
+ if (tmask[i])
+ {
+ seqs.addElement(mask.elementAt(i));
+ }
+
+ return vectorToArray(seqs);
+ }
+
+ /**
+ * Sorts by a given AlignmentOrder object
+ *
+ * @param align Alignment to order
+ * @param order specified order for alignment
+ */
+ 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();
+
+ if (lastOrder == order)
+ {
+ sortOrderAscending = !sortOrderAscending;
+ }
+ else
+ {
+ sortOrderAscending = true;
+ }
+
+ if (sortOrderAscending)
+ {
+ setOrder(align, tmp);
+ }
+ else
+ {
+ setReverseOrder(align,
+ vectorSubsetToArray(tmp, align.getSequences()));
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param align alignment to order
+ * @param tree tree which has
+ *
+ * @return DOCUMENT ME!
+ */
+ private static Vector getOrderByTree(AlignmentI align, NJTree tree)
+ {
+ int nSeq = align.getHeight();
+
+ Vector tmp = new Vector();
+
+ tmp = _sortByTree(tree.getTopNode(), tmp, align.getSequences());
+
+ if (tmp.size() != nSeq)
+ {
+ // TODO: JBPNote - decide if this is always an error
+ // (eg. not when a tree is associated to another alignment which has more
+ // sequences)
+ if (tmp.size() < nSeq)
+ {
+ addStrays(align, tmp);
+ }
+
+ if (tmp.size() != nSeq)
+ {
+ System.err.println("ERROR: tmp.size()=" + tmp.size() +
+ " != nseq=" + nSeq + " in getOrderByTree");
+ }
+ }
+
+ return tmp;
+ }
+
+ /**
+ * Sorts the alignment by a given tree
+ *
+ * @param align alignment to order
+ * @param tree tree which has
+ */
+ public static void sortByTree(AlignmentI align, NJTree tree)
+ {
+ Vector tmp = getOrderByTree(align, tree);
+
+ // tmp should properly permute align with tree.
+ if (lastTree != tree)
+ {
+ sortTreeAscending = true;
+ lastTree = tree;
+ }
+ else
+ {
+ sortTreeAscending = !sortTreeAscending;
+ }
+
+ if (sortTreeAscending)
+ {
+ setOrder(align, tmp);
+ }
+ else
+ {
+ setReverseOrder(align,
+ vectorSubsetToArray(tmp, align.getSequences()));
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param align DOCUMENT ME!
+ * @param seqs DOCUMENT ME!
+ */
+ private static void addStrays(AlignmentI align, Vector seqs)
+ {
+ int nSeq = align.getHeight();
+
+ for (int i = 0; i < nSeq; i++)
+ {
+ if (!seqs.contains(align.getSequenceAt(i)))
+ {
+ seqs.addElement(align.getSequenceAt(i));
+ }
+ }
+
+ if (nSeq != seqs.size())
+ {
+ System.err.println(
+ "ERROR: Size still not right even after addStrays");
+ }
+ }
+
+ /**
+ * 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,
+ Vector seqset)
+ {
+ if (node == null)
+ {
+ return tmp;
+ }
+
+ SequenceNode left = (SequenceNode) node.left();
+ SequenceNode right = (SequenceNode) node.right();
+
+ if ((left == null) && (right == null))
+ {
+ if (!node.isPlaceholder() && (node.element() != null))
+ {
+ if (node.element() instanceof SequenceI)
+ {
+ if (!tmp.contains(node.element()))
+ {
+ tmp.addElement((SequenceI) node.element());
+ }
+ }
+ }
+
+ return tmp;
+ }
+ else
+ {
+ _sortByTree(left, tmp, seqset);
+ _sortByTree(right, tmp, seqset);
+ }
+
+ return tmp;
+ }
+
+ // Ordering Objects
+ // Alignment.sortBy(OrderObj) - sequence of sequence pointer refs in appropriate order
+ //
+
+ /**
+ * recover the order of sequences given by the safe numbering scheme introducd
+ * SeqsetUtils.uniquify.
+ */
+ public static void recoverOrder(SequenceI[] alignment)
+ {
+ float[] ids = new float[alignment.length];
+
+ for (int i = 0; i < alignment.length; i++)
+ ids[i] = (new Float(alignment[i].getName().substring(8))).floatValue();
+
+ jalview.util.QuickSort.sort(ids, alignment);
+ }
+}
git://source.jalview.org / jalview.git / blobdiff