Bits *maskQuerySeq(struct dnaSeq *seq, boolean isProt,
boolean maskQuery, boolean lcMask)
/* Massage query sequence a bit, converting it to correct
* case (upper for protein/lower for DNA) and optionally
* returning upper/lower case info , and trimming poly A. */
{
Bits *qMaskBits = NULL;
verbose(2, "%s\n", seq->name);
if (isProt)
faToProtein(seq->dna, seq->size);
else
{
if (maskQuery)
{
if (lcMask)
toggleCase(seq->dna, seq->size);
qMaskBits = maskFromUpperCaseSeq(seq);
}
faToDna(seq->dna, seq->size);
}
if (seq->size > qWarnSize)
{
warn("Query sequence %s has size %d, it might take a while.",
seq->name, seq->size);
}
return qMaskBits;
}
LetterButton::LetterButton(const QChar& letter, QWidget* parent) :
QPushButton(QString(letter),parent)
{
setCheckable(true);
setAutoDefault(false);
connect(this,SIGNAL(clicked()),this,SLOT(toggleCase()));
skip=true;
}
/*
* Upper case region. Zap all of the lower
* case characters in the region to upper case. Use
* the region code to set the limits. Scan the buffer,
* doing the changes. Call "lineSetChanged" to ensure that
* redisplay is done in all buffers. Bound to
* "C-X C-U".
*/
int
upperRegion(int f, int n)
{
meLine *line ;
int loffs ;
long lline ;
register char c;
register int s;
meRegion region;
if((s=getregion(®ion)) <= 0)
return (s);
if((s=bufferSetEdit()) <= 0) /* Check we can change the buffer */
return s ;
line = frameCur->windowCur->dotLine ;
loffs = frameCur->windowCur->dotOffset ;
lline = frameCur->windowCur->dotLineNo ;
frameCur->windowCur->dotLine = region.line ;
frameCur->windowCur->dotOffset = region.offset ;
frameCur->windowCur->dotLineNo = region.lineNo ;
while (region.size--)
{
if((c = meLineGetChar(frameCur->windowCur->dotLine, frameCur->windowCur->dotOffset)) == '\0')
{
frameCur->windowCur->dotLine = meLineGetNext(frameCur->windowCur->dotLine);
frameCur->windowCur->dotOffset = 0;
frameCur->windowCur->dotLineNo++ ;
}
else
{
if(isLower(c))
{
lineSetChanged(WFMAIN);
#if MEOPT_UNDO
meUndoAddRepChar() ;
#endif
c = toggleCase(c) ;
meLineSetChar(frameCur->windowCur->dotLine, frameCur->windowCur->dotOffset, c);
}
(frameCur->windowCur->dotOffset)++ ;
}
}
frameCur->windowCur->dotLine = line ;
frameCur->windowCur->dotOffset = loffs ;
frameCur->windowCur->dotLineNo = lline ;
return meTRUE ;
}
void Changecase::process()
{
emit startMacro(i18n("Change case"));
if (m_sentenceCaseRadio->isChecked())
sentenceCase();
else if (m_lowerCaseRadio->isChecked())
lowerCase();
else if (m_upperCaseRadio->isChecked())
upperCase();
else if (m_initialCapsRadio->isChecked())
initialCaps();
else if (m_toggleCaseRadio->isChecked())
toggleCase();
emit stopMacro();
}
void bigBlat(struct dnaSeq *untransList, int queryCount, char *queryFiles[], char *outFile, boolean transQuery, boolean qIsDna, FILE *out, boolean showStatus)
/* Run query against translated DNA database (3 frames on each strand). */
{
int frame, i;
struct dnaSeq *seq, trimmedSeq;
struct genoFind *gfs[3];
aaSeq *dbSeqLists[3];
struct trans3 *t3List = NULL;
int isRc;
struct lineFile *lf = NULL;
struct hash *t3Hash = NULL;
boolean forceUpper = FALSE;
boolean forceLower = FALSE;
boolean toggle = FALSE;
boolean maskUpper = FALSE;
ZeroVar(&trimmedSeq);
if (showStatus)
printf("Blatx %d sequences in database, %d files in query\n", slCount(untransList), queryCount);
/* Figure out how to manage query case. Proteins want to be in
* upper case, generally, nucleotides in lower case. But there
* may be repeatMasking based on case as well. */
if (transQuery)
{
if (qMask == NULL)
forceLower = TRUE;
else
{
maskUpper = TRUE;
toggle = !sameString(qMask, "upper");
}
}
else
{
forceUpper = TRUE;
}
if (gvo->fileHead != NULL)
gvo->fileHead(gvo, out);
for (isRc = FALSE; isRc <= 1; ++isRc)
{
/* Initialize local pointer arrays to NULL to prevent surprises. */
for (frame = 0; frame < 3; ++frame)
{
gfs[frame] = NULL;
dbSeqLists[frame] = NULL;
}
t3List = seqListToTrans3List(untransList, dbSeqLists, &t3Hash);
for (frame = 0; frame < 3; ++frame)
{
gfs[frame] = gfIndexSeq(dbSeqLists[frame], minMatch, maxGap, tileSize,
repMatch, ooc, TRUE, oneOff, FALSE, stepSize);
}
for (i=0; i<queryCount; ++i)
{
aaSeq qSeq;
lf = lineFileOpen(queryFiles[i], TRUE);
while (faMixedSpeedReadNext(lf, &qSeq.dna, &qSeq.size, &qSeq.name))
{
dotOut();
/* Put it into right case and optionally mask on case. */
if (forceLower)
toLowerN(qSeq.dna, qSeq.size);
else if (forceUpper)
toUpperN(qSeq.dna, qSeq.size);
else if (maskUpper)
{
if (toggle)
toggleCase(qSeq.dna, qSeq.size);
upperToN(qSeq.dna, qSeq.size);
}
if (qSeq.size > qWarnSize)
{
warn("Query sequence %s has size %d, it might take a while.",
qSeq.name, qSeq.size);
}
trimSeq(&qSeq, &trimmedSeq);
if (transQuery)
transTripleSearch(&trimmedSeq, gfs, t3Hash, isRc, qIsDna, out);
else
tripleSearch(&trimmedSeq, gfs, t3Hash, isRc, out);
gfOutputQuery(gvo, out);
}
lineFileClose(&lf);
}
/* Clean up time. */
trans3FreeList(&t3List);
freeHash(&t3Hash);
for (frame = 0; frame < 3; ++frame)
{
genoFindFree(&gfs[frame]);
}
for (seq = untransList; seq != NULL; seq = seq->next)
{
reverseComplement(seq->dna, seq->size);
}
}
carefulClose(&out);
}
void QsciEditor::setupActions() {
cutAct = new QAction( QIcon::fromTheme( "edit-cut" ), "Cu&t", this );
cutAct->setStatusTip( "Cut the selected text" );
cutAct->setShortcut( tr( "Ctrl+X" ) );
copyAct = new QAction( QIcon::fromTheme( "edit-copy" ), "&Copy", this );
copyAct->setStatusTip( "Copy the selected text" );
copyAct->setShortcut( tr( "Ctrl+C" ) );
pasteAct = new QAction( QIcon::fromTheme( "edit-paste" ), "&Paste", this );
pasteAct->setStatusTip( "Paste the text on the clipboard" );
pasteAct->setShortcut( tr( "Ctrl+V" ) );
deleteAct = new QAction( QIcon::fromTheme( "edit-delete" ), "&Delete", this );
deleteAct->setStatusTip( "Delete the selected Text" );
deleteAct->setShortcut( tr( "Delete" ) );
selectAct = new QAction( QIcon::fromTheme( "edit-select-all" ), "Select &All", this );
selectAct->setStatusTip( "Select all the text" );
selectAct->setShortcut( tr( "Ctrl+A" ) );
deselectAct = new QAction( QIcon(), "Deselect &All", this );
deselectAct->setStatusTip( "Deselect all the text" );
deselectAct->setShortcut( tr( "Ctrl+Shift+A" ) );
undoAct = new QAction( QIcon::fromTheme( "edit-undo" ), "&Undo", this );
undoAct->setStatusTip( "Undo the last change" );
undoAct->setShortcut( tr( "Ctrl+Z" ) );
redoAct = new QAction( QIcon::fromTheme( "edit-redo" ), "&Redo", this );
redoAct->setStatusTip( "Redo the undone change" );
redoAct->setShortcut( tr( "Ctrl+Y" ) );
searchAct = new QAction( QIcon::fromTheme( "edit-find" ), "&Search", this );
searchAct->setStatusTip( "Search the document" );
searchAct->setShortcut( tr( "Ctrl+F" ) );
replaceAct = new QAction( QIcon::fromTheme( "edit-find-replace" ), "&Replace", this );
replaceAct->setStatusTip( "Replace text in the document" );
replaceAct->setShortcut( tr( "Ctrl+R" ) );
changeFontAct = new QAction( QIcon::fromTheme( "preferences-desktop-font" ), "Change &Font", this );
changeFontAct->setStatusTip( "Change the font of the document" );
changeFontAct->setShortcut( tr( "Ctrl+Shift+F" ) );
toggleCaseAct = new QAction( "T&oggle Case of Selection", this );
toggleCaseAct->setStatusTip( "Toggle the case of the selected text" );
toggleCaseAct->setShortcut( tr( "Ctrl+Alt+U" ) );
connect( this, SIGNAL( customContextMenuRequested( const QPoint& ) ), this, SLOT( showCustomMenu( const QPoint& ) ) );
connect( cutAct, SIGNAL( triggered() ), this, SLOT( cutAction() ) );
connect( copyAct, SIGNAL( triggered() ), this, SLOT( copyAction() ) );
connect( pasteAct, SIGNAL( triggered() ), this, SLOT( pasteAction() ) );
connect( deleteAct, SIGNAL( triggered() ), this, SLOT( deleteAction() ) );
connect( undoAct, SIGNAL( triggered() ), this, SLOT( undoAction() ) );
connect( redoAct, SIGNAL( triggered() ), this, SLOT( redoAction() ) );
connect( selectAct, SIGNAL( triggered() ), this, SLOT( selectAction() ) );
connect( deselectAct, SIGNAL( triggered() ), this, SLOT( deselectAction() ) );
connect( changeFontAct, SIGNAL( triggered() ), this, SLOT( changeFont() ) );
connect( toggleCaseAct, SIGNAL( triggered() ), this, SLOT( toggleCase() ) );
connect( searchAct, SIGNAL( triggered() ), this, SLOT( showSearch() ) );
connect( this, SIGNAL( linesChanged() ), this, SLOT( resizeMargins() ) );
addAction( cutAct );
addAction( copyAct );
addAction( pasteAct );
addAction( deleteAct );
addAction( selectAct );
addAction( deselectAct );
addAction( undoAct );
addAction( redoAct );
addAction( searchAct );
addAction( replaceAct );
addAction( changeFontAct );
addAction( toggleCaseAct );
/* Change keyBindings */
SendScintilla( SCI_ASSIGNCMDKEY, SCK_DOWN + ( SCMOD_CTRL << 16 ), SCI_PARADOWN );
SendScintilla( SCI_ASSIGNCMDKEY, SCK_UP + ( SCMOD_CTRL << 16 ), SCI_PARAUP );
SendScintilla( SCI_ASSIGNCMDKEY, SCK_DOWN + ( SCMOD_ALT << 16 ), SCI_LINESCROLLDOWN );
SendScintilla( SCI_ASSIGNCMDKEY, SCK_UP + ( SCMOD_ALT << 16 ), SCI_LINESCROLLUP );
/* Remove Ctrl+D as duplicate line */
SendScintilla( SCI_CLEARCMDKEY, 68 + ( SCMOD_CTRL << 16 ) );
};
