diff TEisotools-1.1.a/commons/core/coord/MergeFromOverlaps.py @ 13:feef9a0db09d draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TEisotools-1.1.a/commons/core/coord/MergeFromOverlaps.py	Wed Jul 20 09:04:42 2016 -0400
@@ -0,0 +1,52 @@
+# Copyright INRA (Institut National de la Recherche Agronomique)
+# http://www.inra.fr
+# http://urgi.versailles.inra.fr
+#
+# This software is governed by the CeCILL license under French law and
+# abiding by the rules of distribution of free software.  You can  use, 
+# modify and/ or redistribute the software under the terms of the CeCILL
+# license as circulated by CEA, CNRS and INRIA at the following URL
+# "http://www.cecill.info". 
+#
+# As a counterpart to the access to the source code and  rights to copy,
+# modify and redistribute granted by the license, users are provided only
+# with a limited warranty  and the software's author,  the holder of the
+# economic rights,  and the successive licensors  have only  limited
+# liability. 
+#
+# In this respect, the user's attention is drawn to the risks associated
+# with loading,  using,  modifying and/or developing or reproducing the
+# software by the user in light of its specific status of free software,
+# that may mean  that it is complicated to manipulate,  and  that  also
+# therefore means  that it is reserved for developers  and  experienced
+# professionals having in-depth computer knowledge. Users are therefore
+# encouraged to load and test the software's suitability as regards their
+# requirements in conditions enabling the security of their systems and/or 
+# data to be ensured and,  more generally, to use and operate it in the 
+# same conditions as regards security. 
+#
+# The fact that you are presently reading this means that you have had
+# knowledge of the CeCILL license and that you accept its terms.
+
+class MergeFromOverlaps(object):
+        
+    def __init__(self, lFeatures):
+        self._lFeaturesToCluster = lFeatures
+        
+    ## Clusterize list of Features implementing isOverlapping() and merge() method (e.g Range-based and MergedRange-based objects).
+    #
+    # @param lUnsorted list of Features unsorted
+    # @return lSortedAndMerged list of Features clustered and sorted
+    #
+    def clusterize(self):
+        lSortedAndMerged = []
+        for iInUnsorted in self._lFeaturesToCluster:
+            toBeRemoved = []
+            for iInSorted in lSortedAndMerged:
+                if iInUnsorted.isOverlapping(iInSorted):
+                    toBeRemoved.append(iInSorted)
+                    iInUnsorted.merge(iInSorted)
+            for tbr in toBeRemoved:
+                lSortedAndMerged.remove(tbr)
+            lSortedAndMerged.append(iInUnsorted)
+        return lSortedAndMerged