\r
protected Vector sequences;\r
protected Vector groups = new Vector();\r
- public Hashtable[] cons;\r
protected char gapCharacter = '-';\r
\r
/** Make an alignment from an array of Sequences.\r
if (current.getLength() > i)\r
{\r
/* MC Should move this to a method somewhere */\r
- if (current.getCharAt(i)!='-' && current.getCharAt(i)!='.' && current.getCharAt(i)!=' ')\r
+ if ( !jalview.util.Comparison.isGap(current.getCharAt(i)))\r
delete = false;\r
\r
}\r
public Vector removeRedundancy(float threshold, Vector sel) {\r
Vector del = new Vector();\r
\r
- for (int i=1; i < sel.size(); i++) {\r
- for (int j = 0; j < i; j++) {\r
+ for (int i = 1; i < sel.size(); i++)\r
+ {\r
+ for (int j = 0; j < i; j++)\r
+ {\r
// Only do the comparison if either have not been deleted\r
- if (!del.contains((SequenceI)sel.elementAt(i)) ||\r
- !del.contains((SequenceI)sel.elementAt(j))) {\r
+ if (!del.contains( (SequenceI) sel.elementAt(i)) ||\r
+ !del.contains( (SequenceI) sel.elementAt(j)))\r
+ {\r
\r
- float pid = Comparison.compare((SequenceI)sel.elementAt(j),\r
- (SequenceI)sel.elementAt(i));\r
+ float pid = Comparison.compare( (SequenceI) sel.elementAt(j),\r
+ (SequenceI) sel.elementAt(i));\r
\r
- if (pid >= threshold) {\r
+ if (pid >= threshold)\r
+ {\r
// Delete the shortest one\r
- if (((SequenceI)sel.elementAt(j)).getSequence().length() >\r
- ((SequenceI)sel.elementAt(i)).getSequence().length()) {\r
+ if ( ( (SequenceI) sel.elementAt(j)).getSequence().length() >\r
+ ( (SequenceI) sel.elementAt(i)).getSequence().length())\r
del.addElement(sel.elementAt(i));\r
- System.out.println("Deleting sequence " + ((SequenceI)sel.elementAt(i)).getName());\r
- } else {\r
+ else\r
del.addElement(sel.elementAt(i));\r
- System.out.println("Deleting sequence " + ((SequenceI)sel.elementAt(i)).getName());\r
- }\r
}\r
}\r
}\r
}\r
\r
// Now delete the sequences\r
- for (int i=0; i < del.size(); i++) {\r
- System.out.println("Deleting sequence " + ((SequenceI)del.elementAt(i)).getName());\r
+ for (int i=0; i < del.size(); i++)\r
deleteSequence((SequenceI)del.elementAt(i));\r
- }\r
\r
return del;\r
}\r
\r
}\r
return null;\r
+ }\r
+\r
+ public SequenceGroup [] findAllGroups(SequenceI s)\r
+ {\r
+\r
+ ArrayList temp = new ArrayList();\r
+\r
+ for (int i = 0; i < this.groups.size();i++)\r
+ {\r
+ SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
+ if (sg.sequences.contains(s))\r
+ temp.add(sg);\r
+ }\r
+\r
+ SequenceGroup [] ret = new SequenceGroup[temp.size()];\r
+ temp.toArray( ret );\r
+\r
+ return ret;\r
\r
}\r
/** */\r
}\r
\r
/** */\r
- public int findIndex(SequenceI s) {\r
+ public int findIndex(SequenceI s)\r
+ {\r
int i=0;\r
- while (i < sequences.size()) {\r
- if (s == getSequenceAt(i)) {\r
+ while (i < sequences.size())\r
+ {\r
+ if (s == getSequenceAt(i))\r
return i;\r
- }\r
+\r
i++;\r
}\r
return -1;\r