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SAM4S [DATASHEET]
11100E–ATARM–24-Jul-13
If all ADC channels (i.e. 16) are used on an application board, there is no restriction of usage of the user sequence. But
as soon as some ADC channels are not enabled for conversion but rather used as pure digital inputs, the respective
indexes of these channels cannot be used in the user sequence fields (ADC_SEQR1, ADC_SEQR2 bitfields). For
example, if channel 4 is disabled (ADC_CSR[4] = 0), ADC_SEQR1, ADC_SEQR2 register bitfields USCH1 up to
USCH16 must not contain the value 4. Thus the length of the user sequence may be limited by this behavior. 
As an example, if only 4 channels over 16 (CH0 up to CH3) are selected for ADC conversions, the user sequence length
cannot exceed 4 channels. Each trigger event may launch up to 4 successive conversions of any combination of
channels 0 up to 3 but no more (i.e. in this case the sequence CH0, CH0, CH1, CH1, CH1 is impossible). 
A sequence that repeats several times the same channel requires more enabled channels than channels actually used
for conversion. For example, a sequence like CH0, CH0, CH1, CH1 requires 4 enabled channels (4 free channels on
application boards) whereas only CH0, CH1 are really converted.
Note:
The reference voltage pins always remain connected in normal mode as in sleep mode.
41.6.7 Comparison Window
The ADC Controller features automatic comparison functions. It compares converted values to a low threshold or a high
threshold or both, according to the CMPMODE function chosen in the Extended Mode Register (ADC_EMR). The
comparison can be done on all channels or only on the channel specified in CMPSEL field of ADC_EMR. To compare all
channels the CMP_ALL parameter of ADC_EMR should be set. 
The flag can be read on the COMPE bit of the Interrupt Status Register (ADC_ISR) and can trigger an interrupt.
The High Threshold and the Low Threshold can be read/write in the Comparison Window Register (ADC_CWR). 
If the comparison window is to be used with LOWRES bit in ADC_MR set to 1, the thresholds do not need to be adjusted
as adjustment will be done internally. Whether or not the LOWRES bit is set, thresholds must always be configured in
consideration of the maximum ADC resolution.
41.6.8 Differential Inputs
The ADC can be used either as a single ended ADC (DIFF bit equal to 0) or as a fully differential ADC (DIFF bit equal to
1) as shown in 
. By default, after a reset, the ADC is in single ended mode. 
If ANACH is set in ADC_MR the ADC can apply a different mode on each channel. Otherwise the parameters of CH0 are
applied to all channels.
The same inputs are used in single ended or differential mode.
In single ended mode, inputs are managed by a 16:1 channels analog multiplexer. In the fully differential mode, inputs
are managed by an 8:1 channels analog multiplexer. See 
.
Table 41-4. Input Pins and Channel Number in Single Ended Mode 
Input Pins
Channel Number
AD0
CH0
AD1
CH1
AD2
CH2
AD3
CH3
AD4
CH4
AD5
CH5
AD6
CH6
AD7
CH7
AD8
CH8
AD9
CH9