Swich to the new version of the progress bar

VERSION

-0.2.0
+0.2.02

python/orgasm/backtranslate/_ahocorasick.pyx

 # cython: language_level=3
 
 from ._ahocorasick cimport *
-from orgasm.utils._progress cimport progressBar
+from orgasm.apps.progress cimport ProgressBar 
+
 from orgasm.utils.dna import reverseComplement
 from ._bitvector cimport BitVector
 
@@ -977,6 +978,7 @@ cdef class ProtAhoCorasick(AhoCorasick):
         cdef size_t  offset
         cdef double* shanonTable = buildShanonTable(readsize,&offset)
         cdef double* shanonLine
+        cdef ProgressBar pb
         
         # mid is the number of read frame globally available for each 
         # protein stored in the automata
@@ -997,7 +999,8 @@ cdef class ProtAhoCorasick(AhoCorasick):
         nuc4 = records + i * (recordsize)
         
         if (progress):
-            progressBar(1,readcount,True)
+            pb=ProgressBar(readcount)
+#            progressBar(1,readcount,True)
 
         while i < readcount:
                 
@@ -1100,7 +1103,7 @@ cdef class ProtAhoCorasick(AhoCorasick):
             i+=1
 
             if (progress):
-                progressBar(i,readcount)
+                pb(i)
 
             while (i< readcount and 
                    samereads(nuc4, nuc4bis, readsize64)):
@@ -1269,7 +1272,7 @@ cdef class NucAhoCorasick(AhoCorasick):
         nuc4 = records + i * (recordsize)
         
         if (progress):
-            progressBar(1,readcount,True)
+            pb=ProgressBar(readcount)
 
         while i < readcount:
                 
@@ -1342,7 +1345,7 @@ cdef class NucAhoCorasick(AhoCorasick):
             i+=1
 
             if (progress):
-                progressBar(i,readcount)
+                pb(i)
 
             while (i< readcount and 
                    samereads(nuc4, nuc4bis, readsize64)):

python/orgasm/multialign/_multi.pyx

@@ -3,7 +3,7 @@
 from collections import Counter
 
 
-from orgasm.utils._progress cimport progressBar
+from orgasm.apps.progress cimport ProgressBar 
 from ._dynamic cimport EndGapFree
 from orgasm.indexer._orgasm cimport Index
 from collections import Counter
@@ -177,6 +177,7 @@ cdef list alignReads(readids,Index index,size_t kmer=12,int smin=10,size_t delta
     cdef size_t h2
     cdef bytes s
     cdef int j                                      # @DuplicatedSignature
+    cdef ProgressBar pb
     
     # We dereplicate the sequences
     for j in readids:
@@ -191,12 +192,12 @@ cdef list alignReads(readids,Index index,size_t kmer=12,int smin=10,size_t delta
     nali = nseq * (nseq-1) // 2
     hashes =[hashSeq(s,kmer) for s in seqs]
     
-    progressBar(1,nali,reset=True,head=bytes("Pairwise alignment %6d x %6d " % (0,0),encoding='ascii'))
+    pb = ProgressBar(nali,head="Pairwise alignment %6d x %6d " % (0,0))
     
     for h1 in range(nseq):
         for h2 in range(h1+1,nseq):
-            
-            progressBar(pos,nali,reset=False,head=bytes("Pairwise alignment %6d x %6d " % (h1,h2),encoding='ascii'))
+            pb.head="Pairwise alignment %6d x %6d " % (h1,h2)
+            pb(pos)
             pos+=1
             
             ali = alignSequence(seqs[h1],seqs[h2],

python/orgasm/version.py

 major = 0
 minor = '2'
-serial= '01'
+serial= '02'
 
 version = "%d.%s.%s" % (major,minor,serial)