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authorMark Sims <mark@nanorex.com>2008-12-21 04:50:00 +0000
committerMark Sims <mark@nanorex.com>2008-12-21 04:50:00 +0000
commitbcc6b3c623bdfd83e7bebfee1de04b3ac7e32c82 (patch)
tree9fe27f8fde1b99e2891b86b6c5fc73e308c1dfee /cad/src/protein/ProteinSequenceEditor
parent39f3c15d8360ae61561866126a2b127fa3b6d48c (diff)
downloadnanoengineer-theirix-bcc6b3c623bdfd83e7bebfee1de04b3ac7e32c82.tar.gz
nanoengineer-theirix-bcc6b3c623bdfd83e7bebfee1de04b3ac7e32c82.zip
This commit includes the following bug fixes:
- In the "Protein Sequence Editor", typing a character in the sequence field works as expected (i.e. cursor position does not skip characters as the user over-types the sequence). - In "Edit Rotamers, the "current residue" is correctly expanded when selecting back and forth b/w peptides. - In "Edit Rotamers, allow the user to unselect the current peptide without clearing the PM (i.e. the unselected peptide remains the current protein), making the UI consistent with Strand Properties. - In "Edit Rotamers, checking "Center view on current residue" should center view immediately.
Diffstat (limited to 'cad/src/protein/ProteinSequenceEditor')
-rw-r--r--cad/src/protein/ProteinSequenceEditor/ProteinSequenceEditor.py224
-rw-r--r--cad/src/protein/ProteinSequenceEditor/Ui_ProteinSequenceEditor.py3
2 files changed, 72 insertions, 155 deletions
diff --git a/cad/src/protein/ProteinSequenceEditor/ProteinSequenceEditor.py b/cad/src/protein/ProteinSequenceEditor/ProteinSequenceEditor.py
index b97368566..045902997 100644
--- a/cad/src/protein/ProteinSequenceEditor/ProteinSequenceEditor.py
+++ b/cad/src/protein/ProteinSequenceEditor/ProteinSequenceEditor.py
@@ -146,12 +146,19 @@ class ProteinSequenceEditor(Ui_ProteinSequenceEditor):
return
self._suppress_textChanged_signal = True
- cursorPosition = self.getCursorPosition()
- theSequence = self.getPlainSequence()
+ cursorPos = self.getCursorPosition()
+ theSequence = self.getPlainSequence()
- theSequence.replace(" ", "G") # Space = G (glycine).
+ if len(theSequence) == len(self._previousSequence):
+ # Replace space characters with the same character.
+ aa = self._previousSequence[cursorPos - 1]
+ theSequence.replace(" ", aa)
+ print "The last character was replaced with: ", aa
- if True: # Set to True for debugging statements.
+ # Insert the sequence; it will be "stylized" by _setSequence().
+ self._setSequence(theSequence, inCursorPos = cursorPos)
+
+ if False: # Set to True for debugging statements.
if theSequence == self._previousSequence:
print "The sequence did not change (YOU SHOULD NEVER SEE THIS)."
elif len(theSequence) < len(self._previousSequence):
@@ -162,21 +169,6 @@ class ProteinSequenceEditor(Ui_ProteinSequenceEditor):
print "Character(s) where added to the sequence."
pass
- # Insert the sequence; it will be "stylized" by _setSequence().
- self._updateSequence(theSequence)
-
- # How has the text changed?
- #if theSequence.length() != 0 and theSequence.length() == self.maxSeqLength:
- #self._updateSequence(theSequence)
- #else:
- ##pop up a message saying that you are not allowed to change the length
- ##of the sequence
- #msg = "Cannot change the length of the sequence."\
- #"You need to have exactly" + str(self.maxSeqLength) + " amino acids."
- #QMessageBox.warning(self.win, "Warning!", msg)
- #self._suppress_textChanged_signal = False
- #return
-
# If the sequence in the text edit (field) is different from the current
# sequence, change the sequence field bg color to pink to
# indicate that the sequence is different. If they are the same,
@@ -269,49 +261,6 @@ class ProteinSequenceEditor(Ui_ProteinSequenceEditor):
outSequence.remove(QRegExp( theString ))
return outSequence
-
- def _updateSequence(self,
- inSequence,
- inRestoreCursor = True):
- """
- Update the sequence (private method)
-
- Note that the callers outside the class should call self.updateSequence,
- but never call this method.
-
- @see: self.setsequence()
- """
- cursor = self.sequenceTextEdit.textCursor()
- cursorMate = self.secStrucTextEdit.textCursor()
- cursorMate2 = self.aaRulerTextEdit.textCursor()
- if cursor.position() == len(self.sequenceTextEdit.toPlainText()):
- selectionStart = 0
- selectionEnd = 0
- elif cursor.position() == -1:
- selectionStart = 0
- selectionEnd = 0
- else:
- selectionStart = cursor.selectionStart()
- selectionEnd = cursor.selectionEnd()
-
- seq = str(inSequence)
- inSequence1 = self._convertProteinSequenceToColoredSequence(seq)
- inSequence1 = self._fixedPitchSequence(inSequence1)
- self.sequenceTextEdit.setHtml( inSequence1 )
-
- #adjust the cursor so that they match for all three text edits
- if inRestoreCursor:
- cursor.setPosition(selectionStart, QTextCursor.MoveAnchor)
- cursor.setPosition(selectionEnd, QTextCursor.KeepAnchor)
- self.sequenceTextEdit.setTextCursor( cursor )
- cursorMate.setPosition( selectionStart, QTextCursor.MoveAnchor )
- cursorMate.setPosition(selectionEnd, QTextCursor.KeepAnchor)
- self.secStrucTextEdit.setTextCursor( cursorMate )
- cursorMate2.setPosition( selectionStart, QTextCursor.MoveAnchor )
- cursorMate2.setPosition(selectionEnd, QTextCursor.KeepAnchor)
- self.aaRulerTextEdit.setTextCursor( cursorMate2 )
-
- return
def clear( self ):
"""
@@ -321,23 +270,34 @@ class ProteinSequenceEditor(Ui_ProteinSequenceEditor):
self._setSequenceAndStructure("", "")
return
- def _setSequenceAndStructure(self, inSequence, inStructure):
+ def _setSequenceAndStructure(self,
+ inSequence,
+ inStructure,
+ inCursorPos = -1):
"""
- Sets the main text edit fields in the following order:
- 1. secondary structure
- 2. ruler
- 3. sequence
- @note: It is important that sequence is set last.
+ Sets the sequence, structure and ruler fields in the sequence editor.
+ @param inSequence: The sequence string.
+ @type inSequence: QString
+ @param inStructure: The secondary structure string.
+ @type inStructure: QString
+ @param inCursorPos: the position in the sequence in which to place the
+ cursor. If cursorPos is negative, the cursor position
+ is placed at first residue of the sequence (default).
+ @type inCursorPos: int
"""
+ #NOTE: It is important that sequence is set last so that setCursorPos()
+ #doesn't complain (i.e. the structure and ruler strings must be
+ #equal to the length of the sequence string before setting the cursor
+ # position). --Mark 2008-12-20
self._setSecondaryStructure(inStructure)
self._setRuler(len(inSequence))
- self._setSequence(inSequence)
+ self._setSequence(inSequence, inCursorPos = inCursorPos)
return
def _setSequence( self,
inSequence,
inStylize = True,
- inRestoreCursor = True
+ inCursorPos = -1
):
"""
Replace the current amino acid sequence with the new sequence text.
@@ -346,7 +306,7 @@ class ProteinSequenceEditor(Ui_ProteinSequenceEditor):
Callers outside this class wishing to update the amino acid sequence
field should call updateSequence().
- @param inSequence: The new sequence.
+ @param inSequence: The sequence string.
@type inSequence: QString
@param inStylize: If True, inSequence will be converted from a plain
@@ -354,20 +314,23 @@ class ProteinSequenceEditor(Ui_ProteinSequenceEditor):
rich text string.
@type inStylize: bool
- @param inRestoreCursor: Not implemented yet.
- @type inRestoreCursor: bool
+ @param inCursorPos: the position in the sequence in which to place the
+ cursor. If cursorPos is negative, the cursor position
+ is placed at first residue of the sequence (default).
+ @type inCursorPos: int
@see: updateSequence()
"""
seq = str(inSequence)
+ seq = seq.upper()
htmlSequence = self._convertProteinSequenceToColoredSequence(seq)
if inStylize:
htmlSequence = self._fixedPitchSequence(htmlSequence)
self._suppress_textChanged_signal = True
self._suppress_cursorPosChanged_signal = True
- self.sequenceTextEdit.setHtml(htmlSequence)
- self.setCursorPosition(inCursorPos = -1) # At the end.
+ self.sequenceTextEdit.setHtml(htmlSequence) # Generates cursorPosChanged signal!
+ self.setCursorPosition(inCursorPos = inCursorPos)
self._suppress_textChanged_signal = False
self._suppress_cursorPosChanged_signal = False
return
@@ -395,7 +358,7 @@ class ProteinSequenceEditor(Ui_ProteinSequenceEditor):
return fixedPitchSequence
- def _setSecondaryStructure(self, inStructure, inRestoreCursor = True):
+ def _setSecondaryStructure(self, inStructure):
"""
Set the secondary structure of the protein. (private method)
@@ -405,64 +368,17 @@ class ProteinSequenceEditor(Ui_ProteinSequenceEditor):
@param inStructure: The structure string.
@type inStructure: QString
- @param inRestoreCursor: restore cursor position
- @type inRestoreCursor: bool
-
@see: updateSequence()
"""
- cursor = self.sequenceTextEdit.textCursor()
- cursorMate = self.secStrucTextEdit.textCursor()
- cursorMate2 = self.aaRulerTextEdit.textCursor()
- if cursor.position() == len(self.sequenceTextEdit.toPlainText()):
- selectionStart = 0
- selectionEnd = 0
- elif cursor.position() == -1:
- selectionStart = 0
- selectionEnd = 0
- else:
- selectionStart = cursor.selectionStart()
- selectionEnd = cursor.selectionEnd()
-
fixedPitchSequence = self._getFormattedSequence(inStructure)
self.secStrucTextEdit.setHtml(fixedPitchSequence)
- if inRestoreCursor:
- cursor.setPosition(selectionStart, QTextCursor.MoveAnchor)
- cursor.setPosition(selectionEnd, QTextCursor.KeepAnchor)
- self.sequenceTextEdit.setTextCursor( cursor )
- cursorMate.setPosition(selectionStart, QTextCursor.MoveAnchor)
- cursorMate.setPosition(selectionEnd, QTextCursor.KeepAnchor)
- self.secStrucTextEdit.setTextCursor( cursorMate )
- cursorMate2.setPosition(selectionStart, QTextCursor.MoveAnchor)
- cursorMate2.setPosition(selectionEnd, QTextCursor.KeepAnchor)
- self.aaRulerTextEdit.setTextCursor( cursorMate2 )
return
- def _setRuler(self, lengthOfSeq, inRestoreCursor = True):
+ def getRulerText(self, lengthOfSeq):
+ """
+ Return the ruler text given I{lengthOfSeq} (i.e. the length of the
+ current sequence).
"""
- Set the sequence ruler for up to three digits.
-
- Callers outside this class wishing to update the ruler
- should call updateSequence().
-
- @param lengthOfSeq: length of the sequence.
- @type lengthOfSeq: int
-
- @param inRestoreCursor: restore cursor position
- @type inRestoreCursor: bool
- """
- cursor = self.sequenceTextEdit.textCursor()
- cursorMate = self.secStrucTextEdit.textCursor()
- cursorMate2 = self.aaRulerTextEdit.textCursor()
- if cursor.position() == len(self.sequenceTextEdit.toPlainText()):
- selectionStart = 0
- selectionEnd = 0
- elif cursor.position() == -1:
- selectionStart = 0
- selectionEnd = 0
- else:
- selectionStart = cursor.selectionStart()
- selectionEnd = cursor.selectionEnd()
-
rulerText = ""
i = 0
while i < lengthOfSeq:
@@ -486,19 +402,24 @@ class ProteinSequenceEditor(Ui_ProteinSequenceEditor):
else:
rulerText = rulerText + "-"
i = i + 1
+ return rulerText
+
+ def _setRuler(self, lengthOfSeq):
+ """
+ Set the sequence ruler with a length of I{lengthOfSeq}.
+
+ Callers outside this class wishing to update the ruler
+ should call updateSequence().
+
+ @param lengthOfSeq: length of the sequence.
+ @type lengthOfSeq: int
+
+ @note: supports up to 3 digits (i.e. max length of 999).
+ """
+ rulerText = self.getRulerText(lengthOfSeq)
fixedPitchSequence = "<html><bold><font size=3 face=Courier New color=green>" + rulerText
fixedPitchSequence += "</font></bold></html>"
self.aaRulerTextEdit.setHtml(fixedPitchSequence)
- if inRestoreCursor:
- cursor.setPosition(selectionStart, QTextCursor.MoveAnchor)
- cursor.setPosition(selectionEnd, QTextCursor.KeepAnchor)
- self.sequenceTextEdit.setTextCursor( cursor )
- cursorMate.setPosition(selectionStart, QTextCursor.MoveAnchor)
- cursorMate.setPosition(selectionEnd, QTextCursor.KeepAnchor)
- self.secStrucTextEdit.setTextCursor( cursorMate )
- cursorMate2.setPosition(selectionStart, QTextCursor.MoveAnchor)
- cursorMate2.setPosition(selectionEnd, QTextCursor.KeepAnchor)
- self.aaRulerTextEdit.setTextCursor( cursorMate2 )
return
def _convertProteinSequenceToColoredSequence(self, inSequence):
@@ -568,7 +489,7 @@ class ProteinSequenceEditor(Ui_ProteinSequenceEditor):
outLength = theSequence.length()
return outLength
- def updateSequence(self, proteinChunk = None, cursorPos = -1):
+ def updateSequence(self, proteinChunk = None, inCursorPos = -1):
"""
Updates the sequence editor with the sequence of I{proteinChunk}.
@@ -576,10 +497,10 @@ class ProteinSequenceEditor(Ui_ProteinSequenceEditor):
(default), the sequence editor is cleared.
@type proteinChunk: protein Chunk
- @param cursorPos: the position in the sequence in which to place the
+ @param inCursorPos: the position in the sequence in which to place the
cursor. If cursorPos is negative, the cursor position
- is placed at the end of the sequence (default).
- @type cursorPos: int
+ is placed at first residue of the sequence (default).
+ @type inCursorPos: int
"""
if proteinChunk:
@@ -596,10 +517,7 @@ class ProteinSequenceEditor(Ui_ProteinSequenceEditor):
# We have a protein chunk. Update the editor with its sequence.
sequence = self.current_protein.protein.get_sequence_string()
structure = self.current_protein.protein.get_secondary_structure_string()
- self._setSequenceAndStructure(sequence, structure)
-
- # Set cursor position.
- self.setCursorPosition(inCursorPos = cursorPos)
+ self._setSequenceAndStructure(sequence, structure, inCursorPos = inCursorPos)
# Update the bg color to white.
self._sequence_changed = False
@@ -626,14 +544,14 @@ class ProteinSequenceEditor(Ui_ProteinSequenceEditor):
@param inCursorPos: the position in the sequence in which to place the
cursor. If cursorPos is negative, the cursor position
- is placed at the end of the sequence (default).
+ is placed at the beginning of the sequence (default).
@type inCursorPos: int
"""
# Make sure cursorPos is in the valid range.
if inCursorPos < 0:
- cursorPos = self.getSequenceLength() - 1
- anchorPos = self.getSequenceLength()
+ cursorPos = 0
+ anchorPos = 1
elif inCursorPos >= self.getSequenceLength():
cursorPos = self.getSequenceLength() - 1
anchorPos = self.getSequenceLength()
@@ -644,6 +562,8 @@ class ProteinSequenceEditor(Ui_ProteinSequenceEditor):
# Useful print statements for debugging.
print "setCursorPosition(): Sequence=", self.getPlainSequence()
print "setCursorPosition(): Final inCursorPos=%d\ncursorPos=%d, anchorPos=%d" % (inCursorPos, cursorPos, anchorPos)
+
+ self._suppress_cursorPosChanged_signal = True
# Finally, set the cursor position in the sequence.
cursor = self.sequenceTextEdit.textCursor()
@@ -660,6 +580,8 @@ class ProteinSequenceEditor(Ui_ProteinSequenceEditor):
cursorMate2.setPosition(anchorPos, QTextCursor.MoveAnchor)
cursorMate2.setPosition(cursorPos, QTextCursor.KeepAnchor)
self.aaRulerTextEdit.setTextCursor( cursorMate2 )
+
+ self._suppress_cursorPosChanged_signal = False
return
@@ -684,9 +606,7 @@ class ProteinSequenceEditor(Ui_ProteinSequenceEditor):
cursorPos = cursor.position()
print "_cursorPosChanged(): Here! cursorPos=", cursorPos
- self._suppress_cursorPosChanged_signal = True
self.setCursorPosition(inCursorPos = cursorPos) # sets all three.
- self._suppress_cursorPosChanged_signal = False
# Provide amino acid info as cursor position changes
env.history.statusbar_msg("")
@@ -769,7 +689,7 @@ class ProteinSequenceEditor(Ui_ProteinSequenceEditor):
sequence = lines[0]
sequence = QString(sequence)
sequence = sequence.toUpper()
- self._updateSequence(sequence)
+ self._setSequence(sequence)
return
def _write_FASTA_File(self, fileName, sequence):
@@ -967,7 +887,7 @@ class ProteinSequenceEditor(Ui_ProteinSequenceEditor):
self.sequenceTextEdit.setTextCursor(cursor)
#Set the sequence in the text edit.
- self._updateSequence(sequence)
+ self._setSequence(sequence)
#Find the next occurance of the 'seqrchString' in the sequence.
self.findNext()
diff --git a/cad/src/protein/ProteinSequenceEditor/Ui_ProteinSequenceEditor.py b/cad/src/protein/ProteinSequenceEditor/Ui_ProteinSequenceEditor.py
index 3b6380932..662109eba 100644
--- a/cad/src/protein/ProteinSequenceEditor/Ui_ProteinSequenceEditor.py
+++ b/cad/src/protein/ProteinSequenceEditor/Ui_ProteinSequenceEditor.py
@@ -14,9 +14,6 @@ TODO:
- NFR: Add "Position" field.
- NFR: Load sequence for the current peptide from a FASTA file.
- NFR: Save sequence for the current peptide to a FASTA file.
-
-BUGS:
-- Typing a character in the sequence moves the cursor, skipping the next character.
"""
from PyQt4.Qt import QToolButton
generated by cgit v1.2.3 (git 2.39.1) at 2025-04-14 12:41:21 +0000