+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+*\r
+* This program is free software; you can redistribute it and/or\r
+* modify it under the terms of the GNU General Public License\r
+* as published by the Free Software Foundation; either version 2\r
+* of the License, or (at your option) any later version.\r
+*\r
+* This program is distributed in the hope that it will be useful,\r
+* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+* GNU General Public License for more details.\r
+*\r
+* You should have received a copy of the GNU General Public License\r
+* along with this program; if not, write to the Free Software\r
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+*/\r
package jalview.analysis;\r
\r
import jalview.datamodel.*;\r
+\r
import jalview.util.*;\r
-import jalview.io.*;\r
\r
import java.util.*;\r
\r
+\r
/** Data structure to hold and manipulate a multiple sequence alignment\r
*/\r
-public class AlignmentSorter {\r
-\r
- private AlignmentSorter() {\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
+public class AlignmentSorter\r
+{\r
+ static boolean sortIdAscending = true;\r
+ static int lastGroupHash = 0;\r
+ static boolean sortGroupAscending = true;\r
+ static AlignmentOrder lastOrder = null;\r
+ static boolean sortOrderAscending = true;\r
+ static NJTree lastTree = null;\r
+ static boolean sortTreeAscending = true;\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
+ {\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
+ {\r
+ scores[i] = Comparison.PID(align.getSequenceAt(i).getSequence(),\r
+ s.getSequence());\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
- 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
+ * Reverse the order of the sort\r
+ *\r
+ * @param align DOCUMENT ME!\r
+ * @param seqs DOCUMENT ME!\r
+ */\r
+ private static void setReverseOrder(AlignmentI align, SequenceI[] seqs)\r
+ {\r
+ int nSeq = seqs.length;\r
+\r
+ int len = 0;\r
+\r
+ if ((nSeq % 2) == 0)\r
+ {\r
+ len = nSeq / 2;\r
+ }\r
+ else\r
+ {\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
+ {\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
- // align.setGroups(newg);\r
- }\r
+ /**\r
+ * Sets the Alignment object with the given sequences\r
+ *\r
+ * @param align Alignment object to be updated\r
+ * @param tmp sequences as a vector\r
+ */\r
+ private static void setOrder(AlignmentI align, Vector tmp)\r
+ {\r
+ setOrder(align, vectorSubsetToArray(tmp, align.getSequences()));\r
+ }\r
\r
- /** */\r
- public static void sortByPID(AlignmentI align, SequenceI s) {\r
- int nSeq = align.getHeight();\r
+ /**\r
+ * Sets the Alignment object with the given sequences\r
+ *\r
+ * @param align DOCUMENT ME!\r
+ * @param seqs sequences as an array\r
+ */\r
+ public static void setOrder(AlignmentI align, SequenceI[] seqs)\r
+ {\r
+ // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work\r
+ Vector algn = align.getSequences();\r
+ Vector tmp = new Vector();\r
\r
- float scores[] = new float[nSeq];\r
- SequenceI seqs[] = new SequenceI[nSeq];\r
+ for (int i = 0; i < seqs.length; i++)\r
+ {\r
+ if(algn.contains(seqs[i]))\r
+ tmp.addElement(seqs[i]);\r
+ }\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
+ algn.removeAllElements();\r
+ //User may have hidden seqs, then clicked undo or redo\r
+ for (int i = 0; i < tmp.size(); i++)\r
+ {\r
+ algn.addElement(tmp.elementAt(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
+ * Sorts by ID. Numbers are sorted before letters.\r
+ *\r
+ * @param align The alignment object to sort\r
+ */\r
+ public static void sortByID(AlignmentI align)\r
+ {\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
+ {\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
+ {\r
+ setReverseOrder(align, seqs);\r
+ }\r
+ else\r
+ {\r
+ setOrder(align, seqs);\r
+ }\r
+\r
+ sortIdAscending = !sortIdAscending;\r
}\r
- }\r
-\r
- private static void setOrder(AlignmentI align, Vector tmp) {\r
- setOrder(align,vectorToArray(tmp));\r
- }\r
\r
- private static void setOrder(AlignmentI align, SequenceI [] seqs) {\r
-// NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work\r
- for (int i = 0; i < seqs.length; i++) {\r
- align.getSequences().setElementAt(seqs[i],i);\r
+ /**\r
+ * Sorts the alignment by size of group.\r
+ * <br>Maintains the order of sequences in each group\r
+ * by order in given alignment object.\r
+ *\r
+ * @param align sorts the given alignment object by group\r
+ */\r
+ public static void sortByGroup(AlignmentI align)\r
+ {\r
+ //MAINTAINS ORIGNAL SEQUENCE ORDER,\r
+ //ORDERS BY GROUP SIZE\r
+ Vector groups = new Vector();\r
+\r
+ if (groups.hashCode() != lastGroupHash)\r
+ {\r
+ sortGroupAscending = true;\r
+ lastGroupHash = groups.hashCode();\r
+ }\r
+ else\r
+ {\r
+ sortGroupAscending = !sortGroupAscending;\r
+ }\r
+\r
+ //SORTS GROUPS BY SIZE\r
+ //////////////////////\r
+ for (int i = 0; i < align.getGroups().size(); i++)\r
+ {\r
+ SequenceGroup sg = (SequenceGroup) align.getGroups().elementAt(i);\r
+\r
+ for (int j = 0; j < groups.size(); j++)\r
+ {\r
+ SequenceGroup sg2 = (SequenceGroup) groups.elementAt(j);\r
+\r
+ if (sg.getSize(false) > sg2.getSize(false))\r
+ {\r
+ groups.insertElementAt(sg, j);\r
+\r
+ break;\r
+ }\r
+ }\r
+\r
+ if (!groups.contains(sg))\r
+ {\r
+ groups.addElement(sg);\r
+ }\r
+ }\r
+\r
+ //NOW ADD SEQUENCES MAINTAINING ALIGNMENT ORDER\r
+ ///////////////////////////////////////////////\r
+ Vector seqs = new Vector();\r
+\r
+ for (int i = 0; i < groups.size(); i++)\r
+ {\r
+ SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
+ SequenceI[] orderedseqs = sg.getSequencesInOrder(align);\r
+\r
+ for (int j = 0; j < orderedseqs.length; j++)\r
+ {\r
+ seqs.addElement(orderedseqs[j]);\r
+ }\r
+ }\r
+\r
+ if (sortGroupAscending)\r
+ {\r
+ setOrder(align, seqs);\r
+ }\r
+ else\r
+ {\r
+ setReverseOrder(align,\r
+ vectorSubsetToArray(seqs, align.getSequences()));\r
+ }\r
}\r
- }\r
\r
- /** */\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
+ * Converts Vector to array.\r
+ * java 1.18 does not have Vector.toArray()\r
+ *\r
+ * @param tmp Vector of SequenceI objects\r
+ *\r
+ * @return array of Sequence[]\r
+ */\r
+ private static SequenceI[] vectorToArray(Vector tmp)\r
+ {\r
+ SequenceI[] seqs = new SequenceI[tmp.size()];\r
+\r
+ for (int i = 0; i < tmp.size(); i++)\r
+ {\r
+ seqs[i] = (SequenceI) tmp.elementAt(i);\r
+ }\r
+\r
+ return seqs;\r
}\r
\r
- QuickSort.sort(ids,seqs);\r
-\r
- setReverseOrder(align,seqs);\r
- }\r
-\r
- public static void sortByGroup(AlignmentI align) {\r
- int nSeq = align.getHeight();\r
- Vector groups = align.getGroups();\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
+ * DOCUMENT ME!\r
+ *\r
+ * @param tmp DOCUMENT ME!\r
+ * @param mask DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ private static SequenceI[] vectorSubsetToArray(Vector tmp, Vector mask)\r
+ {\r
+ Vector seqs = new Vector();\r
+ int i;\r
+ boolean[] tmask = new boolean[mask.size()];\r
+\r
+ for (i = 0; i < mask.size(); i++)\r
+ tmask[i] = true;\r
+\r
+ for (i = 0; i < tmp.size(); i++)\r
+ {\r
+ Object sq = tmp.elementAt(i);\r
+\r
+ if (mask.contains(sq) && tmask[mask.indexOf(sq)])\r
+ {\r
+ tmask[mask.indexOf(sq)] = false;\r
+ seqs.addElement(sq);\r
+ }\r
+ }\r
+\r
+ for (i = 0; i < tmask.length; i++)\r
+ if (tmask[i])\r
+ {\r
+ seqs.addElement(mask.elementAt(i));\r
+ }\r
+\r
+ return vectorToArray(seqs);\r
}\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
+ * Sorts by a given AlignmentOrder object\r
+ *\r
+ * @param align Alignment to order\r
+ * @param order specified order for alignment\r
+ */\r
+ public static void sortBy(AlignmentI align, AlignmentOrder order)\r
+ {\r
+ // Get an ordered vector of sequences which may also be present in align\r
+ Vector tmp = order.getOrder();\r
+\r
+ if (lastOrder == order)\r
+ {\r
+ sortOrderAscending = !sortOrderAscending;\r
+ }\r
+ else\r
+ {\r
+ sortOrderAscending = true;\r
+ }\r
+\r
+ if (sortOrderAscending)\r
+ {\r
+ setOrder(align, tmp);\r
+ }\r
+ else\r
+ {\r
+ setReverseOrder(align,\r
+ vectorSubsetToArray(tmp, align.getSequences()));\r
+ }\r
}\r
\r
- setOrder(align,seqs);\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param align alignment to order\r
+ * @param tree tree which has\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ private static Vector getOrderByTree(AlignmentI align, NJTree tree)\r
+ {\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
+ if (tmp.size() < nSeq)\r
+ {\r
+ addStrays(align, tmp);\r
+ }\r
+\r
+ if (tmp.size() != nSeq)\r
+ {\r
+ System.err.println("ERROR: tmp.size()=" + tmp.size() +\r
+ " != nseq=" + nSeq + " in getOrderByTree");\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
+ return tmp;\r
}\r
- return seqs;\r
- }\r
-\r
- public static void sortByTree(AlignmentI align, NJTree tree) {\r
- int nSeq = align.getHeight();\r
\r
- Vector tmp = new Vector();\r
-\r
- tmp = _sortByTree(tree.getTopNode(),tmp);\r
+ /**\r
+ * Sorts the alignment by a given tree\r
+ *\r
+ * @param align alignment to order\r
+ * @param tree tree which has\r
+ */\r
+ public static void sortByTree(AlignmentI align, NJTree tree)\r
+ {\r
+ Vector tmp = getOrderByTree(align, tree);\r
+\r
+ // tmp should properly permute align with tree.\r
+ if (lastTree != tree)\r
+ {\r
+ sortTreeAscending = true;\r
+ lastTree = tree;\r
+ }\r
+ else\r
+ {\r
+ sortTreeAscending = !sortTreeAscending;\r
+ }\r
+\r
+ if (sortTreeAscending)\r
+ {\r
+ setOrder(align, tmp);\r
+ }\r
+ else\r
+ {\r
+ setReverseOrder(align,\r
+ vectorSubsetToArray(tmp, align.getSequences()));\r
+ }\r
+ }\r
\r
- if (tmp.size() != nSeq) {\r
- System.err.println("ERROR: tmp.size() != nseq in sortByTree");\r
- if (tmp.size() < nSeq) {\r
- addStrays(align,tmp);\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param align DOCUMENT ME!\r
+ * @param seqs DOCUMENT ME!\r
+ */\r
+ private static void addStrays(AlignmentI align, Vector seqs)\r
+ {\r
+ int nSeq = align.getHeight();\r
+\r
+ for (int i = 0; i < nSeq; i++)\r
+ {\r
+ if (!seqs.contains(align.getSequenceAt(i)))\r
+ {\r
+ seqs.addElement(align.getSequenceAt(i));\r
+ }\r
+ }\r
+\r
+ if (nSeq != seqs.size())\r
+ {\r
+ System.err.println(\r
+ "ERROR: Size still not right even after addStrays");\r
+ }\r
}\r
\r
- setOrder(align,tmp);\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param node DOCUMENT ME!\r
+ * @param tmp DOCUMENT ME!\r
+ * @param seqset DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ private static Vector _sortByTree(SequenceNode node, Vector tmp,\r
+ Vector seqset)\r
+ {\r
+ if (node == null)\r
+ {\r
+ return tmp;\r
+ }\r
+\r
+ SequenceNode left = (SequenceNode) node.left();\r
+ SequenceNode right = (SequenceNode) node.right();\r
+\r
+ if ((left == null) && (right == null))\r
+ {\r
+ if (!node.isPlaceholder() && (node.element() != null))\r
+ {\r
+ if (node.element() instanceof SequenceI)\r
+ {\r
+ if (!tmp.contains(node.element()))\r
+ {\r
+ tmp.addElement((SequenceI) node.element());\r
+ }\r
+ }\r
+ }\r
+\r
+ return tmp;\r
+ }\r
+ else\r
+ {\r
+ _sortByTree(left, tmp, seqset);\r
+ _sortByTree(right, tmp, seqset);\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
+ return tmp;\r
}\r
- }\r
\r
- public static Vector _sortByTree(SequenceNode node, Vector tmp) {\r
- if (node == null) {return tmp;}\r
+ // Ordering Objects\r
+ // Alignment.sortBy(OrderObj) - sequence of sequence pointer refs in appropriate order\r
+ //\r
\r
- SequenceNode left = (SequenceNode)node.left();\r
- SequenceNode right = (SequenceNode)node.right();\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
+ {\r
+ float[] ids = new float[alignment.length];\r
\r
- if (left == null && right == null) {\r
- if (node.element() instanceof SequenceI) {\r
- tmp.addElement((SequenceI)node.element());\r
- return tmp;\r
- }\r
- } else {\r
- _sortByTree(left,tmp);\r
- _sortByTree(right,tmp);\r
+ for (int i = 0; i < alignment.length; i++)\r
+ ids[i] = (new Float(alignment[i].getName().substring(8))).floatValue();\r
+\r
+ jalview.util.QuickSort.sort(ids, alignment);\r
}\r
- return tmp;\r
- }\r
}\r
git://source.jalview.org / jalview.git / blobdiff