\r
import jalview.datamodel.*;\r
\r
-import jalview.io.*;\r
-\r
import jalview.util.*;\r
\r
import java.util.*;\r
\r
/** Data structure to hold and manipulate a multiple sequence alignment\r
*/\r
-public class AlignmentSorter {\r
- /** */\r
+public class AlignmentSorter\r
+{\r
static boolean sortIdAscending = true;\r
static int lastGroupHash = 0;\r
static boolean sortGroupAscending = true;\r
* @param align AlignmentI\r
* @param s SequenceI\r
*/\r
- public static void sortByPID(AlignmentI align, SequenceI s) {\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
+ for (int i = 0; i < nSeq; i++)\r
+ {\r
scores[i] = Comparison.PID(align.getSequenceAt(i), s);\r
seqs[i] = align.getSequenceAt(i);\r
}\r
setReverseOrder(align, seqs);\r
}\r
\r
- private static void setReverseOrder(AlignmentI align, SequenceI[] seqs) {\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
+ if ((nSeq % 2) == 0)\r
+ {\r
len = nSeq / 2;\r
- } else {\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
+ 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
- private static void setOrder(AlignmentI align, Vector tmp) {\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
- private static void setOrder(AlignmentI align, SequenceI[] seqs) {\r
-\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
+ private 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
+\r
for (int i = 0; i < seqs.length; i++)\r
{\r
- algn.setElementAt(seqs[i], i);\r
+ algn.setElementAt(seqs[i], i);\r
}\r
}\r
\r
- public static void sortByID(AlignmentI align) {\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
+ 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
+ if (sortIdAscending)\r
+ {\r
setReverseOrder(align, seqs);\r
- } else {\r
+ }\r
+ else\r
+ {\r
setOrder(align, seqs);\r
}\r
\r
sortIdAscending = !sortIdAscending;\r
}\r
\r
- public static void sortByGroup(AlignmentI align) {\r
- //MAINTAINS ORIGNAL SEQUENCE ORDER,\r
- //ORDERS BY GROUP SIZE\r
-\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
+ if (groups.hashCode() != lastGroupHash)\r
+ {\r
sortGroupAscending = true;\r
lastGroupHash = groups.hashCode();\r
- } else {\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
+ 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
- if(sg.getSize() > sg2.getSize())\r
- {\r
- groups.insertElementAt(sg, j);\r
- break;\r
- }\r
- }\r
-\r
- if (!groups.contains(sg))\r
- {\r
- groups.addElement(sg);\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() > sg2.getSize())\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
+ 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
+ if (sortGroupAscending)\r
+ {\r
setOrder(align, seqs);\r
- } else {\r
+ }\r
+ else\r
+ {\r
setReverseOrder(align,\r
vectorSubsetToArray(seqs, align.getSequences()));\r
}\r
}\r
\r
- private static SequenceI[] vectorToArray(Vector tmp) {\r
-\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
+ for (int i = 0; i < tmp.size(); i++)\r
+ {\r
seqs[i] = (SequenceI) tmp.elementAt(i);\r
}\r
\r
return seqs;\r
}\r
\r
- private static SequenceI[] vectorSubsetToArray(Vector tmp, Vector mask) {\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
for (i = 0; i < mask.size(); i++)\r
tmask[i] = true;\r
\r
- for (i = 0; i < tmp.size(); i++) {\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
\r
for (i = 0; i < tmask.length; i++)\r
- if (tmask[i]) {\r
+ if (tmask[i])\r
+ {\r
seqs.addElement(mask.elementAt(i));\r
}\r
\r
return vectorToArray(seqs);\r
}\r
\r
- public static void sortBy(AlignmentI align, AlignmentOrder order) {\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
+ if (lastOrder == order)\r
+ {\r
sortOrderAscending = !sortOrderAscending;\r
- } else {\r
+ }\r
+ else\r
+ {\r
sortOrderAscending = true;\r
}\r
\r
- if (sortOrderAscending) {\r
+ if (sortOrderAscending)\r
+ {\r
setOrder(align, tmp);\r
- } else {\r
+ }\r
+ else\r
+ {\r
setReverseOrder(align,\r
vectorSubsetToArray(tmp, align.getSequences()));\r
}\r
}\r
\r
- public static Vector getOrderByTree(AlignmentI align, NJTree tree) {\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
+ 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
+ if (tmp.size() < nSeq)\r
+ {\r
addStrays(align, tmp);\r
}\r
\r
- if (tmp.size() != nSeq) {\r
+ if (tmp.size() != nSeq)\r
+ {\r
System.err.println("ERROR: tmp.size()=" + tmp.size() +\r
" != nseq=" + nSeq + " in getOrderByTree");\r
}\r
return tmp;\r
}\r
\r
- public static void sortByTree(AlignmentI align, NJTree tree) {\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
+ if (lastTree != tree)\r
+ {\r
sortTreeAscending = true;\r
lastTree = tree;\r
- } else {\r
+ }\r
+ else\r
+ {\r
sortTreeAscending = !sortTreeAscending;\r
}\r
\r
- if (sortTreeAscending) {\r
+ if (sortTreeAscending)\r
+ {\r
setOrder(align, tmp);\r
- } else {\r
+ }\r
+ else\r
+ {\r
setReverseOrder(align,\r
vectorSubsetToArray(tmp, align.getSequences()));\r
}\r
}\r
\r
- private static void addStrays(AlignmentI align, Vector seqs) {\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
- if (!seqs.contains(align.getSequenceAt(i))) {\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
+ if (nSeq != seqs.size())\r
+ {\r
System.err.println(\r
"ERROR: Size still not right even after addStrays");\r
}\r
}\r
\r
- public static Vector _sortByTree(SequenceNode node, Vector tmp,\r
- Vector seqset) {\r
- if (node == null) {\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
- if (!node.isPlaceholder() && (node.element() != null)) {\r
- if (node.element() instanceof SequenceI) {\r
- if (!tmp.contains(node.element())) {\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
- } else {\r
+ }\r
+ else\r
+ {\r
_sortByTree(left, tmp, seqset);\r
_sortByTree(right, tmp, seqset);\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
+ public static void recoverOrder(SequenceI[] alignment)\r
+ {\r
float[] ids = new float[alignment.length];\r
\r
for (int i = 0; i < alignment.length; i++)\r
git://source.jalview.org / jalview.git / blobdiff