// -----------------------------------------------------------------------------
// CTestSDKHierarchicalLists::TestHLSCLSetTextCIL
// -----------------------------------------------------------------------------
TInt CTestSDKHierarchicalLists::TestHLSCLSetTextCIL( CStifItemParser& /*aItem*/ )
{
CTestControl* control = CTestControl::NewL();
CleanupStack::PushL( control );
STIF_ASSERT_NOT_NULL( control );
CAknSingleColumnStyleTreeList* treeList = CAknSingleColumnStyleTreeList::NewLC( *control );
STIF_ASSERT_NOT_NULL( treeList );
_LIT( KFirstColumn, "FirstColumn" );
TBuf<KLength> firstColumn( KFirstColumn );
_LIT( KSecondColumn, "SecondColumn" );
TUint32 flags = CAknSingleColumnStyleTreeList::EPersistent;
TAknTreeItemID id = treeList->AddCoreDataRowL( KAknTreeIIDRoot, firstColumn, KSecondColumn, flags, ETrue );
STIF_ASSERT_NOT_EQUALS( 0, id );
_LIT( KFirstColumnSet, "Change" );
TBuf<KLength> textSet( KFirstColumnSet );
treeList->SetTextL( id, textSet, 0, ETrue );
TBuf<KLength> firstColumnGet = treeList->Text( id, 0 );
STIF_ASSERT_EQUALS( 0, firstColumnGet.Compare( textSet ) );
CleanupStack::PopAndDestroy( treeList );
CleanupStack::PopAndDestroy( control );
return KErrNone;
}
// AbacusRefine
//
// ctgcns - from=0 to=-1 level=abAbacus_Smooth
// - from=0 to=-1 level=abAbacus_Poly_X
// - from=0 to=-1 level=abAbacus_Indel
// utgcns - same
//
// from,to are C-style. Used to be INCLUSIVE, but never used anyway
//
int32
abMultiAlign::refine(abAbacus *abacus,
abAbacusRefineLevel level,
uint32 from, // from and to are in ma's column coordinates
uint32 to) {
if (length() < to)
to = length();
abColID sid = columnList[from]; // id of the starting column
abColID eid = columnList[to - 1]; // id of the ending column
assert(sid == firstColumn());
assert(eid == lastColumn());
abColumn *start_column = abacus->getColumn(sid);
abColID stab_bgn;
uint32 score_reduction = 0;
while (start_column->ident() != eid) {
int32 window_width = IdentifyWindow(abacus, start_column, stab_bgn, level);
// start_column stands as the candidate for first column in window
// look for window start and stop
if (window_width > 0) {
// If the first column, insert a gap column for maneuvering room
if (start_column->prevID().isValid() == false) {
abBeadID firstbeadID = abacus->getBead(start_column->callID() )->downID();
abBeadID newbeadID = abacus->appendGapBead(abacus->getBead(firstbeadID)->ident());
fprintf(stderr, "Adding gapbead "F_U32" after "F_U32" to add abacus room for abutting left of multialignment\n",
newbeadID.get(), firstbeadID.get());
abacus->appendColumn(abacus->getBead(firstbeadID)->colIdx(), newbeadID);
}
// if the window is too big, there's likely a polymorphism that won't respond well to abacus,
// so skip it.
//
// BPW saw crashes with large window_width's (1333, 3252, 1858, 675, 855, 1563, 601, 1102).
// The longest window_width that worked was 573. Previous versions used 100 here. Not sure
// what it should be.
//
if (window_width < MAX_WINDOW_FOR_ABACUS_REFINE)
score_reduction += refineWindow(abacus, start_column, stab_bgn);
start_column = abacus->getColumn(stab_bgn);
}
start_column = abacus->getColumn(stab_bgn);
}
// WITH quality=1 make_v_list=1, all the rest defaults
abacus->refreshMultiAlign(ident(), true, true);
return(score_reduction);
}
