from CCP4ReportParser import *

class mrbump_basic_report(Report):
  # Specify which gui task and/or pluginscript this applies to
  TASKNAME = 'mrbump_basic'
  RUNNING = True
  CSS_VERSION = '0.1.0'

  def __init__(self,xmlnode=None,jobInfo={},**kw):
    Report. __init__(self,xmlnode=xmlnode,jobInfo=jobInfo,cssVersion=self.CSS_VERSION,**kw)
  
    import CCP4Utils,os
    
    mrbump=self.xmlnode.select("//MRBUMP")


    results = self.addResults()
    results.append( 'MrBUMP is a pipeline to trial many search models in molecular replacement. It will find and prepate possible search models based on a sequence alignment between your target sequence and that of known structures in the PDB (using Phmmer by default). It then goes on to run molecular replacement (MR) on the best of these. Post MR it refine each resulting solution and do some initial model building to assess the likely success or otherwise of the molecular replacement search.' )

    tableFoldsearch = results.addFold(label='sequence-based search results', initiallyOpen=True)
    tableFoldsearch.append('These are the results of the sequence based search (using Phmmer). Below is the alignment of the best matches to the target sequences.<br/>')

    jobDirectory = jobInfo['fileroot']
    
    if not os.path.isfile(os.path.join(jobDirectory, "search_mrbump_1", "logs", "alignment_report.log")):
        results.append("Warning: Cannot find alignment report file!")
    else: 
        alog=open(os.path.join(jobDirectory, "search_mrbump_1", "logs", "alignment_report.log"), "r")
        lines="".join(alog.readlines())
        alog.close()
        tableFoldsearch.append("<pre>%s</pre>" % lines)

    #stuff=tableFoldsearch.addTable(select="//MRBUMP/target_details/Sequence_align_list")
    #for title, select in [ ["Chain ID", "alignment/chainID"],
    #                       ["Alignment", "alignment/sequence"] ] :
    #    stuff.addData(title=title, select=select)
#
#    tableFoldx = results.addFold(label='detailed results for MR model search and preparation', initiallyOpen=True)
#    tableFoldx.append('Target Sequence:')
#    tableFoldx.append('Scores:')
#    tableFoldx.append('List of search results:')
#    tableFoldx.append('List of prepared models:')
#    tablex =  tableFoldx.addTable(select="//MRBUMP/model_name/mrprogram")
#    for title, select in [ ["Model Name", "SearchModel_name"] ] :
#        tablex.addData(title=title, select=select)

    tableFoldsearch = results.addFold(label='search model preparation', initiallyOpen=True)
    tableFoldsearch.append('These are the search models that have been prepared for use in Molecular Replacement.<br/>')

    if not os.path.isfile(os.path.join(jobDirectory, "search_mrbump_1", "logs", "model_report.log")):
        results.append("Models will be listed shortly..")
    else: 
        alog=open(os.path.join(jobDirectory, "search_mrbump_1", "logs", "model_report.log"), "r")
        lines="".join(alog.readlines())
        alog.close()
        tableFoldsearch.append("<pre>%s</pre>" % lines)

    tableFoldmr = results.addFold(label='detailed results for molecular replacement and refinement', initiallyOpen=True)

    tableFoldmr.append('Model names have the following format: source PDB_chain ID_MR preparation method. Each model is used in Phaser to do molecular replacement. \
                      The resulting MR solution is then refined with Refmac (Final R, Final R) and SHELXE may be run to do density \
                      modification and c-alpha tracing (SHELXE CC).<br/>')

    if not os.path.isfile(os.path.join(jobDirectory, "search_mrbump_1", "results", "results.txt")):
        results.append("Molecular replacement results will appear here soon...")
    else: 
        alog=open(os.path.join(jobDirectory, "search_mrbump_1", "results", "results.txt"), "r")
        #lines="".join(alog.readlines())
        lines=alog.readlines()
        alog.close()

        CAPTURE=False
        results_string=""
        for line in lines:
            if "############" in line and CAPTURE == False:
                CAPTURE=True
            if CAPTURE and "$$" in line[0:2]:
                CAPTURE=False
                break
            if CAPTURE:
                results_string+=line

        tableFoldmr.append("<pre>%s</pre>" % results_string)

#    table1 =  tableFoldmr.addTable(select="//MRBUMP/model_name/mrprogram")
#
#    for title, select in [ ["Model Name", "SearchModel_name"],
#                           ["Phaser LLG", "PHASER_LLG"],
#                           ["Phaser TFZ", "PHASER_TFZ"],
#                           ["Final R<sub>fact</sub>", "final_Rfact"],
#                           ["Final R<sub>free</sub>", "final_Rfree"],
#                           ["SHELXE CC", "SHELXE_CC"] ] :
#
#        table1.addData(title=title, select=select)

    self.addTaskReferences()

if __name__ == "__main__":
  import sys
  mrbump_basic_report(xmlFile=sys.argv[1],jobId=sys.argv[2])