[Chimera-users]

[Eric Pettersen]

Hi Sabuj,
     I've appended a context diff for MAV's SeqCanvas.py file.  It  
makes the ruler use the ungapped numbering of the first sequence.   
For positions where there is a gap in the first sequence it uses  
'?'.  I think this is what you wanted, but let me know if I got that  
wrong.
     On another note, the new AL2CO conservation measures in the  
1.2154 snapshot don't work on the Mac and possibly on Linux  
(depending on your execution path).  If you want to get them to work,  
I've also appended a context diff for Conservation.py below and have  
also made the entire replacement file available at http:// 
www.cgl.ucsf.edu/home/pett/chimera/Conservation.py (which, on a Mac,  
you put in Chimera.app/Contents/Resources/share/MultAlignViewer  
[which you may have to use Terminal.app to access] and on Linux in  
<your install dir>/share/MultAlignViewer).

--Eric

On Aug 9, 2005, at 10:04 AM, Pattanayek, Sabuj wrote:

> Hi all,
>
> Is there a modification I can do to the multi-align viewer code so  
> that "-"
> (gaps) characters are not counted in the alignment numbering (but  
> are still
> displayed for alignment purposes) from a fasta file in the multi- 
> align viewer?
> The numbering should correspond to the first sequence found in the  
> fasta file
> (i.e. I don't care about the numbering due to gaps in the second,  
> third, etc
> sequences).
>
> Thanks,
> Sabuj Pattanayek
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>

*** SeqCanvas.py        6 Aug 2005 00:08:50 -0000       1.59
--- SeqCanvas.py        9 Aug 2005 17:57:45 -0000
***************
*** 1056,1063 ****

                 end = min(self.seqOffset + self.lineWidth, len 
(self.seqs[0]))
                 for chunkStart in range(self.seqOffset, end, 10):
                         text = self.mainCanvas.create_text(x, y,  
anchor='s',
!                               font=self.font, text="%d" %  
(chunkStart+1))
                         self.rulerTexts.append(text)
                         x += self.chunkGap + 10 * (self.fontPixels[0]
                                                         +  
self.letterGaps[0])
--- 1056,1068 ----

                 end = min(self.seqOffset + self.lineWidth, len 
(self.seqs[0]))
                 for chunkStart in range(self.seqOffset, end, 10):
+                       seq1index = self.seqs[0].gapped2ungapped 
(chunkStart)
+                       if seq1index is None:
+                               dispText = "?"
+                       else:
+                               dispText = str(seq1index+1)
                         text = self.mainCanvas.create_text(x, y,  
anchor='s',
!                               font=self.font, text="%s" % (dispText))
                         self.rulerTexts.append(text)
                         x += self.chunkGap + 10 * (self.fontPixels[0]
                                                         +  
self.letterGaps[0])


*** Conservation.py     3 Aug 2005 20:19:15 -0000       1.16
--- Conservation.py     9 Aug 2005 18:28:45 -0000
***************
*** 56,62 ****
                 tf = open(tfName, "w")
                 save(tf, None, self.seqs, None)
                 tf.close()
!               command = "al2co -i %s -f %d -c %d -w %d -g %g" %  
(tfName,
                         prefs[AL2CO_FREQ], prefs[AL2CO_CONS],
                         prefs[AL2CO_WINDOW], prefs[AL2CO_GAP])
                 if prefs[AL2CO_CONS] == 2:
--- 56,65 ----
                 tf = open(tfName, "w")
                 save(tf, None, self.seqs, None)
                 tf.close()
!               import os, os.path
!               chimeraRoot = os.environ.get("CHIMERA")
!               command = os.path.join(chimeraRoot, 'bin', 'al2co') + \
!                       " -i %s -f %d -c %d -w %d -g %g" % (tfName,
                         prefs[AL2CO_FREQ], prefs[AL2CO_CONS],
                         prefs[AL2CO_WINDOW], prefs[AL2CO_GAP])
                 if prefs[AL2CO_CONS] == 2: