#print i, j
ids = cl.getClusterSeqIds(i, j)
#print ids
color = mc.getColor(i, j)
#print color
cdata = clusterData.clusterData(ids, color, seqStrings)
print "cluster count: ", len(cdata.clustSeqs)
if len(cdata.clustSeqs) > 0:
print "print"
drawCluster.drawCluster(i, j, color, cdata.clustSeqs)
# draw color chart
myplot = plot3.plot3(rows,cols, myColorMap)
report = Report.Report()
report.saveToFile(docPath, numIter, rows, cols, clusterid, myColorMap)
sigma68error = 0 #No sigma68error yet
#print "Sigma68 = %4.5f" % (sigma68)
#print "Number of objects in that bin: %d \n" %(len(catbins))
results[i,z_index,j] = rangez/bins*i + rangez/(2*bins)
results[i,rms_index,j] = rms
results[i,rms_index+1,j] = rmserror
results[i,sigma68_index,j] = sigma68
results[i,sigma68_index+1,j] = sigma68error
if j<1:
results[i,comp_index,j] = 1
norm_counts[i] = len(catbins)
if j>0:
results[i,comp_index,j] = ((float) (len(catbins)))/((float) (norm_counts[i]))
else:
#print "No objects in that bin"
results[i,z_index,j] = rangez/bins*i + rangez/(2*bins)
results[i,rms_index:comp_index+1,j] = nan
#Calling to plots
plot1.plot1(results)
plot2.plot2(cat)
plot3.plot3(cat)
plot4.plot4(cat)
#Finish measuring the elapsed time
end = time.time()
elapsed = end - start
print "Elapsed time: %4.1f seconds\n" % (elapsed)
#import seqData
#import Bio
#import Bio.AlignIO
#from Bio import SeqIO
#from Bio.Seq import Seq
import plot3
import mapcolors
if __name__ == '__main__' :
#
rows = 4
cols = 3
mc = mapcolors.mapcolors()
colors = mc.colors3
plot3.plot3(rows,cols, colors)
