Download [#UGENE-4816] Replacing of characters in alignment

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[UGENE-4816] Replacing of characters in alignment Created: 13/Oct/15
Updated:
27/Jan/16 Resolved: 09/Nov/15
Status:
Project:
Component/s:
Affects
Version/s:
Fix Version/s:
Closed
UGENE
view-msa
1.18
Type:
Reporter:
Resolution:
Labels:
Remaining
Estimate:
Time Spent:
Original
Estimate:
New Feature
Olga Golosova
Fixed
prerelease
Not Specified
Issue Links:
Relates
relates to
relates to
relates to
relates to
relates to
Story Points:
Assigned Tester:
Tests Type:
Epic Link:
Sprint:
Affect Type:
1.20
Priority:
Assignee:
Votes:
Blocker
Artyom Savchenko
0
Not Specified
Not Specified
UGENE-1340
UGENE-4804
UGENE-4906
UGENE-4834
UGENE-4833
Editing characters in the Alignment E...
Incosistent alphabet deriving for ali...
Incosistent alphabet deriving for ali...
Alphabets of visualized objects
Incosistent alphabet deriving for ali...
Open
Closed
Closed
Open
Closed
13
Denis Kandrov
GUI automatic
Editing alignment
DEV-10/11/2015
Userdefined
Description
It must be possible to replace characters in a multiple alignment, opened in the Alignment
Editor.
Use case 1:
1. Open an alignment in the Alignment Editor.
2. Select one character (e.g. this is character 'A').
Expected result: the character is selected in the normal mode (i.e. borders of the
character are drawn using a dashed line).
3. Press Shift + R keys on the keyboard.
Expected result: the character is selected in the replacement mode (i.e. the border of the
character are drawn using another color and/or bold).
4. Press a key on the keyboard with another character of the same alphabet (e.g C key).
Expected result: the original character of the alignment was replaced with the new one
(e.g 'A' was replaced with 'C'). Selection is in normal mode.
Use case 2:
1. Open an alignment in the Alignment Editor.
2. Select one character (e.g. this is character 'A').
Expected result: the character is selected in the normal mode.
3. Open the context menu in the sequence area.
Expected result: the menu contains an item "Edit > Replace character". The item is
enabled. A hotkey Shift+R is shown nearby.
4. Select the item.
Expected result: the character is selected in the replacement mode.
5. Press a key on the keyboard with another character of the same alphabet. Use a lowercase character (e.g c key).
Expected result: the original character of the alignment was replaced with the new one,
converted to upper-case (e.g 'A' was replaced with 'C'). Selection is in normal mode.
Use case 3:
The same as UC2, except use item "Actions > Edit > Replace character" in the UGENE main
menu.
Use case 4:
1. Open an alignment in the Alignment Editor.
2. Select a region with more than one character.
3. Open the context menu in the sequence area.
Expected result: the "Edit > Replace character" item is disabled. Selection is in normal
mode.
4. Open "Actions > Edit" in the main menu.
Expected result: the "Replace character" item is disabled. Selection is in normal mode.
5. Press Shift + R keys on the keyboard.
Expected result: Nothing happens. Selection is in normal mode.
Use case 5:
1. Open an alignment in the Alignment Editor.
2. Replace a character by another one, so that the alphabet of the alignment has changed
(alphabets are changed according to the rules, described in ).
Expected result:
o The original character was replaced by the new one.
o The alphabet of the alignment has been changed.
o A warning notification appears:
The alignment has been modified, so that its alphabet has been
switched from "%1" to "%2". Use "Undo", if you'd like to restore
the original alignment.
Here "%1" is one of the values: "Standard DNA", "Extended DNA", "Standard
RNA", "Extended RNA", "Standard amino acid", "Extended amino acid",
"Raw".
Use case 6:
1. Open an alignment in the Alignment Editor.
2. Replace a character by another one, so that the alphabet of the alignment has changed.
Expected result: The warning notification appears.
3. Click "Undo".
Expected state: There is NO notifications.
4. Click "Redo".
Expected state: The warning notification appears again.
Use case 7:
1. Open an alignment of the "Standard amino acid" alphabet in the Alignment Editor.
2. Replace a character by 'A' (the 'A' character is included both into nucleotide and amino
acid alphabets).
Expected result:
o The original character was replaced by the new one.
o The alphabet is still the same.
o There is NO notifications.
Use case 8:
1. Open an alignment.
2. Select a character and make active the replacement mode for it.
3. Click another character in the alignment.
Expected result: the first character is no more in the replacement mode.
Use case 9:
1. Open an alignment.
2. Select a character and make active the replacement mode for it.
3. Open the Options Panel.
Expected result: the character is no more in the replacement mode.
Use case 10:
1. Open an alignment.
2. Select a character and make active the replacement mode for it.
3. Click somewhere else inside the Alignment Editor window.
Expected result: the character is no more in the replacement mode.
Use case 11:
1.
2.
3.
4.
5.
Open a sequence.
Open an alignment.
Select a character and make active the replacement mode for it.
Open the window with sequence.
Open back the Alignment Editor window.
Expected result: the character is no more in the replacement mode.
Use case 12:
1. Open an alignment.
2. Select a character and make active the replacement mode for it.
3. Replace the character by another character not from "A..Z a..z - –" character set.
Expected result:
o An error notification appears:
It is not possible to insert the character into the alignment. Please
use a character from set A-Z (upper-case or lower-case) or the
gap character ('Space', '-', or '–').
o
o
The original character was not modified.
The replacement mode is NO MORE active.
Comments
Comment by Artyom Savchenko [ 26/Oct/15 ]
Test plan:
https://ugene.unipro.ru/wiki/pages/viewpage.action?pageId=17465751&focusedCommentId=17465761#comme
17465761
Comment by Olga Golosova [ 29/Oct/15 ]
Please make sure that the added UC6 works properly.
The use case has been added for consistency as similar use case was added to .
Comment by Denis Kandrov [ 10/Nov/15 ]
Tested.
Comment by Yuliya Algaer [ 27/Jan/16 ]
Reviewed.
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