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I have a screen where I get a List of Main items. Inturn, each of these main items will have list of sub items inside them.

Now user can select a Main Item or items inside it and then run the report. This will generate a chart for each item selected (in our case 7 lines on chart).In my view this is not a good user experience as the list of sub items can grow really long and user has to scroll through.

Please not there is no relationship between the main item selection and child items. When we select Main item,it does not select all the child items beneath it.

An alternate , I could think of is having a side tab for each Main item and the show the Sub items on right side.

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This is very specific and I must say that the intuitiveness of the final solution may be suffering a little from this specificity. But, at the same time, I think you are looking more towards professional Users rather than newbies. Therefore, intuitiveness may not be the first priority here and you should put efficiency of use I the first place.

With that said, what I would do:

  • I would minimise the indents to save space. Instead, I would use different styling for groups and support them with just some minimal [+]/[-] expand/contract button - just guessing that the names can be quite descriptive and need more space.

  • Double clicking on groups might expand or contract them.

  • You could consider contracting a group as another one is expanded.

  • I might move the checkboxes to the right (although it would need to be at least corridor tested) to wash out this “all items in group selected” feeling, and support it with a label somewhere in the top part of the interface.

  • While contracted, a group should show “3 sub items selected”

  • I would also consider a separate place in the interface showing all the selected items, since as you said the lists can be very long. Maybe on top of the whole thing.

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