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Test table fixes
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bosborne committed Jul 6, 2016
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15 changes: 7 additions & 8 deletions howtos/Beginners_HOWTO.md
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Expand Up @@ -361,6 +361,7 @@ To set or assign a value:
$seq_obj->seq("MMTYDFFFFVVNNNNPPPPAAAW");
```

The table below shows the methods you're likely to use with the Sequence object directly. Bear in mind that not all values, such as `molecule` or `division`, are found in all sequence formats, you have to know something about your input sequences in order to get some of these values.

|--------+-----------+------------+--------|
| Name | Returns | Example | Note |
Expand Down Expand Up @@ -392,18 +393,16 @@ $seq_obj->seq("MMTYDFFFFVVNNNNPPPPAAAW");

Table 1. Sequence objects method.

The table above shows the methods you're likely to use with the Sequence object directly. Bear in mind that not all values, such as `molecule` or `division`, are found in all sequence formats, you have to know something about your input sequences in order to get some of these values.

There are also a number of methods that are concerned with the Features and Annotations associated with the Sequence object. This is something of a tangent but if you'd like to learn more see the [Feature-Annotation HOWTO](Features_and_Annotations_HOWTO.html). The methods related to this topic are shown below.

|--------+-----------+------------|
| Name | Returns | Note |
|-----------------------|----------------|--------------------|
| get_SeqFeatures | array of SeqFeature objects | |
| Name | Returns | Note |
|--------|-----------|------------|
| get_SeqFeatures | array of SeqFeature objects | |
| get_all_SeqFeatures | array of SeqFeature objects array | includes sub-features |
| remove_SeqFeatures | array of SeqFeatures removed | |
| feature_count | number of SeqFeature objects | |
| add_SeqFeature | annotation array of Annotation objects | get or set |
| remove_SeqFeatures | array of SeqFeatures removed | |
| feature_count | number of SeqFeature objects | |
| add_SeqFeature | annotation array of Annotation objects | get or set |
|--------+-----------+------------|
Table 2. Feature and Annotation methods.

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