* 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
-\r
package jalview.analysis;\r
\r
import jalview.datamodel.*;\r
-import jalview.util.*;\r
+\r
import jalview.io.*;\r
\r
+import jalview.util.*;\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
- try\r
- {\r
- jbInit();\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
+ private AlignmentSorter() {\r
+ try {\r
+ jbInit();\r
+ } catch (Exception ex) {\r
+ ex.printStackTrace();\r
+ }\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
+ 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
- float[] arr = new float [nGroup];\r
- Object[] s = new Object[nGroup];\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
- for (int i=0; i < nGroup; i++) {\r
- arr[i] = ((SequenceGroup)groups.elementAt(i)).getSize();\r
- s[i] = groups.elementAt(i);\r
+ QuickSort.sort(arr, s);\r
+\r
+ // align..setGroups(newg);\r
}\r
\r
- QuickSort.sort(arr,s);\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
- // align..setGroups(newg);\r
- }\r
+ float[] scores = new float[nSeq];\r
+ SequenceI[] seqs = new SequenceI[nSeq];\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
+ for (int i = 0; i < nSeq; i++) {\r
+ scores[i] = Comparison.PID(align.getSequenceAt(i), s);\r
+ seqs[i] = align.getSequenceAt(i);\r
+ }\r
\r
- float scores[] = new float[nSeq];\r
- SequenceI seqs[] = new SequenceI[nSeq];\r
+ QuickSort.sort(scores, 0, scores.length - 1, seqs);\r
\r
- for (int i = 0; i < nSeq; i++) {\r
- scores[i] = Comparison.PID(align.getSequenceAt(i),s);\r
- seqs[i] = align.getSequenceAt(i);\r
+ setReverseOrder(align, seqs);\r
}\r
\r
- QuickSort.sort(scores,0,scores.length-1,seqs);\r
+ private static void setReverseOrder(AlignmentI align, SequenceI[] seqs) {\r
+ int nSeq = seqs.length;\r
+\r
+ int len = 0;\r
\r
- setReverseOrder(align,seqs);\r
- }\r
+ if ((nSeq % 2) == 0) {\r
+ len = nSeq / 2;\r
+ } else {\r
+ len = (nSeq + 1) / 2;\r
+ }\r
\r
- private static void setReverseOrder(AlignmentI align, SequenceI [] seqs) {\r
- int nSeq = seqs.length;\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
- int len = 0;\r
- if (nSeq%2 == 0) {\r
- len = nSeq/2;\r
- } else {\r
- len = (nSeq+1)/2;\r
+ private static void setOrder(AlignmentI align, Vector tmp) {\r
+ setOrder(align, vectorSubsetToArray(tmp, align.getSequences()));\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
+ private static void setOrder(AlignmentI align, SequenceI[] seqs) {\r
+ // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work\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
\r
- private static void setOrder(AlignmentI align, Vector tmp) {\r
- setOrder(align,vectorSubsetToArray(tmp, align.getSequences()));\r
- }\r
+ public static void sortByID(AlignmentI align) {\r
+ int nSeq = align.getHeight();\r
\r
- private static void setOrder(AlignmentI align, SequenceI [] seqs) {\r
- // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work\r
+ String[] ids = new String[nSeq];\r
+ SequenceI[] seqs = new SequenceI[nSeq];\r
\r
- Vector algn = align.getSequences();\r
+ for (int i = 0; i < nSeq; i++) {\r
+ ids[i] = align.getSequenceAt(i).getName();\r
+ seqs[i] = align.getSequenceAt(i);\r
+ }\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
+ QuickSort.sort(ids, seqs);\r
\r
- String ids[] = new String[nSeq];\r
- SequenceI seqs[] = new SequenceI[nSeq];\r
+ if (sortIdAscending) {\r
+ setReverseOrder(align, seqs);\r
+ } else {\r
+ setOrder(align, seqs);\r
+ }\r
\r
- for (int i = 0; i < nSeq; i++) {\r
- ids[i] = align.getSequenceAt(i).getName();\r
- seqs[i] = align.getSequenceAt(i);\r
+ sortIdAscending = !sortIdAscending;\r
}\r
\r
- QuickSort.sort(ids,seqs);\r
+ public static void sortByGroup(AlignmentI align) {\r
+ Vector groups = align.getGroups();\r
+\r
+ if (groups.hashCode() != lastGroupHash) {\r
+ sortGroupAscending = true;\r
+ lastGroupHash = groups.hashCode();\r
+ } else {\r
+ sortGroupAscending = !sortGroupAscending;\r
+ }\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
+ /*\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,\r
+ vectorSubsetToArray(seqs, align.getSequences()));\r
+ }\r
+ }\r
+\r
+ private static SequenceI[] vectorToArray(Vector tmp) {\r
+ SequenceI[] seqs = new SequenceI[tmp.size()];\r
\r
- if(sortIdAscending)\r
- setReverseOrder(align,seqs);\r
- else\r
- setOrder(align, seqs);\r
+ for (int i = 0; i < tmp.size(); i++) {\r
+ seqs[i] = (SequenceI) tmp.elementAt(i);\r
+ }\r
+\r
+ return seqs;\r
+ }\r
\r
- sortIdAscending = !sortIdAscending;\r
- }\r
- static int lastGroupHash = 0;\r
- static boolean sortGroupAscending = true;\r
+ private static SequenceI[] vectorSubsetToArray(Vector tmp, Vector mask) {\r
+ Vector seqs = new Vector();\r
+ int i;\r
+ int m;\r
+ int p;\r
+ boolean[] tmask = new boolean[m = mask.size()];\r
\r
- public static void sortByGroup(AlignmentI align) {\r
- Vector groups = align.getGroups();\r
- if (groups.hashCode()!=lastGroupHash) {\r
- sortGroupAscending=true;\r
- lastGroupHash = groups.hashCode();\r
- } else\r
- sortGroupAscending = ! sortGroupAscending;\r
+ for (i = 0; i < m; i++)\r
+ tmask[i] = true;\r
\r
- Vector seqs = new Vector();\r
+ for (i = 0; i < tmp.size(); i++) {\r
+ Object sq;\r
\r
- for (int i=0; i < groups.size(); i++) {\r
- SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
+ if (mask.contains(sq = tmp.elementAt(i))) {\r
+ tmask[mask.indexOf(sq)] = false;\r
+ seqs.addElement(sq);\r
+ m--;\r
+ }\r
+ }\r
\r
- for (int j = 0; j < sg.getSize(); j++) {\r
- seqs.addElement(sg.getSequenceAt(j));\r
- }\r
+ for (i = 0; i < tmask.length; i++)\r
+ if (tmask[i]) {\r
+ seqs.addElement(mask.elementAt(i));\r
+ }\r
+\r
+ return vectorToArray(seqs);\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
+ 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
+\r
+ // if (tmp.size()<align.getHeight())\r
+ // addStrays(align, tmp);\r
+ if (lastOrder == order) {\r
+ sortOrderAscending = !sortOrderAscending;\r
+ } else {\r
+ sortOrderAscending = true;\r
+ }\r
+\r
+ if (sortOrderAscending) {\r
+ setOrder(align, tmp);\r
+ } else {\r
+ setReverseOrder(align,\r
+ vectorSubsetToArray(tmp, align.getSequences()));\r
+ }\r
}\r
-*/\r
- if(sortGroupAscending)\r
- setOrder(align,seqs);\r
- else\r
- setReverseOrder( align, vectorSubsetToArray(seqs, align.getSequences()));\r
\r
- }\r
+ public static Vector getOrderByTree(AlignmentI align, NJTree tree) {\r
+ int nSeq = align.getHeight();\r
\r
- private static SequenceI [] vectorToArray(Vector tmp) {\r
- SequenceI[] seqs = new SequenceI[tmp.size()];\r
+ Vector tmp = new Vector();\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
+ tmp = _sortByTree(tree.getTopNode(), tmp, align.getSequences());\r
\r
+ if (tmp.size() != nSeq) {\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
+ addStrays(align, tmp);\r
+ }\r
+\r
+ if (tmp.size() != nSeq) {\r
+ System.err.println("ERROR: tmp.size()=" + tmp.size() +\r
+ " != nseq=" + nSeq + " in getOrderByTree");\r
+ }\r
+ }\r
+\r
+ return tmp;\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
+ public static void sortByTree(AlignmentI align, NJTree tree) {\r
+ Vector tmp = getOrderByTree(align, tree);\r
+\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
+\r
+ if (sortTreeAscending) {\r
+ setOrder(align, tmp);\r
+ } else {\r
+ setReverseOrder(align,\r
+ vectorSubsetToArray(tmp, align.getSequences()));\r
+ }\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
+ private static void addStrays(AlignmentI align, Vector seqs) {\r
+ int nSeq = align.getHeight();\r
+\r
+ for (int i = 0; i < nSeq; i++) {\r
+ if (!seqs.contains(align.getSequenceAt(i))) {\r
+ seqs.addElement(align.getSequenceAt(i));\r
+ }\r
+ }\r
+\r
+ if (nSeq != seqs.size()) {\r
+ System.err.println(\r
+ "ERROR: Size still not right even after addStrays");\r
+ }\r
}\r
- if (nSeq != seqs.size()) {\r
- System.err.println("ERROR: Size still not right even after addStrays");\r
+\r
+ public static Vector _sortByTree(SequenceNode node, Vector tmp,\r
+ Vector seqset) {\r
+ if (node == null) {\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
+ tmp.addElement((SequenceI) node.element());\r
+ }\r
+ }\r
+ }\r
+\r
+ return tmp;\r
+ } else {\r
+ _sortByTree(left, tmp, seqset);\r
+ _sortByTree(right, tmp, seqset);\r
+ }\r
+\r
+ return tmp;\r
}\r
- }\r
\r
- public static Vector _sortByTree(SequenceNode node, Vector tmp, Vector seqset) {\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
+ float[] ids = new float[alignment.length];\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
+ for (int i = 0; i < alignment.length; i++)\r
+ ids[i] = (new Float(alignment[i].getName().substring(8))).floatValue();\r
\r
- } else {\r
- _sortByTree(left,tmp, seqset);\r
- _sortByTree(right,tmp, seqset);\r
+ jalview.util.QuickSort.sort(ids, alignment);\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
+ private void jbInit() throws Exception {\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff