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trickyck merged 4 commits into from
May 25, 2022
Merged

Added keyboard syntax plus other minor changes #35

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ede468b
added keyboard syntax plus other minor changes such as adding full st…
trickyck May 25, 2022
63e95e6
Merge branch 'staging' into add_keyboard_syntax
tapaswenipathak May 25, 2022
ca8e5f2
added spaces between symbols as discussed
trickyck May 25, 2022
044d0da
Merge branch 'add_keyboard_syntax' of https://github.com/greengypsy/O…
trickyck May 25, 2022
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2 changes: 1 addition & 1 deletion docs/topp/ini-file-editor.md
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Expand Up @@ -3,7 +3,7 @@ INIFileEditor

Can be used to visually edit INI files of TOPP tools.

The values can be edited by double-clicking or pressing F2.
The values can be edited by double-clicking or pressing <kbd>F2</kbd>.

The documentation of each value is shown in the text area on the bottom of the widget.

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2 changes: 1 addition & 1 deletion docs/tutorials/TOPP/data-editing-in-toppview.md
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Expand Up @@ -8,4 +8,4 @@ After enabling the feature editing mode in the context menu of the feature layer
- Features can be dragged with the mouse in order to change the m/z and RT position.
- The position, intensity and charge of a feature can be edited by double-clicking a feature.
- Features can be created by double-clicking the layer background.
- Features can be removed by selecting them and pressing the DEL key.
- Features can be removed by selecting them and pressing the <kbd>DEL</kbd> key.
80 changes: 40 additions & 40 deletions docs/tutorials/TOPP/hotkeys-table.md
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Expand Up @@ -5,71 +5,71 @@ TOPPView Hotkeys

| Hotkey | Function |
|----------------------|-----------------------------------------------------|
| `CTRL+O` | Open file |
| `CTRL+W` | Close current window |
| `CTRL+S` | Save current layer |
| `CTRL+SHIFT+S` | Save visible data of current layer |
| <kbd>CTRL</kbd> + <kbd>O</kbd> | Open file |
| <kbd>CTRL</kbd> + <kbd>W</kbd> | Close current window |
| <kbd>CTRL</kbd> + <kbd>S</kbd> | Save current layer |
| <kbd>CTRL</kbd> + <kbd>SHIFT</kbd> + <kbd>S</kbd> | Save visible data of current layer |


## Navigation in the data

| Hotkey | Function |
|----------------------|-----------------------------------------------------|
| `CTRL` | Activate zoom mode |
| `SHIFT` | Activate measurement mode |
| `Arrow keys` | Translate currently shown data (1D View: Shift + Left/Right moves to the next peak in sparse data)|
| `CTRL++`, `CTRL+- | Move up and down in zoom history |
| <kbd>CTRL</kbd> | Activate zoom mode |
| <kbd>SHIFT</kbd> | Activate measurement mode |
| <kbd>Arrow keys</kbd> | Translate currently shown data (1D View: <kbd>Shift</kbd> + <kbd>Left</kbd>/<kbd>Right</kbd> moves to the next peak in sparse data)|
|<kbd>CTRL</kbd> + <kbd>+</kbd>, <br><kbd>CTRL</kbd> + <kbd>-</kbd> | Move up and down in zoom history |
| Mouse wheel | Move up and down in zoom history |
| `CTRL+G` | Goto dialog |
| `Backspace` | Reset zoom |
| `PageUp` | Select previous layer |
| `PageDown` | Select next layer |
| <kbd>CTRL</kbd> + <kbd>G</kbd> | Go to dialog |
| <kbd>Backspace</kbd> | Reset zoom |
| <kbd>PageUp</kbd> | Select previous layer |
| <kbd>PageDown</kbd> | Select next layer |

## Visalization options
## Visualization options

| Hotkey | Function |
|----------------------|-----------------------------------------------------|
| `CTRL+R` | Show/hide grid lines |
| `CTRL+L` | Show/hide axis legends |
| `N` | Intensity mode: Normal |
| `P` | Intensity mode: Perecentage |
| `S` | Intensity mode: Snam-to-maximum |
| `I` | 1D draw mode: peaks |
| `R` | 1D draw mode: raw data |
| `CTRL`+`ALT`+`Home` | 2D draw mode: increase minimum canvas coverage threshold (for raw peak scaling)|
| `CTRL`+`ALT`+`End` | 2D draw mode: decrease minimum canvas coverage threshold (for raw peak scaling) |
| `CTRL`+`ALT`+`+` | 2D draw mode: increase maximum point size (for raw peak scaling) |
| `CTRL`+`ALT`+`-` | 2D draw mode: decrease maximum point size (for raw peak scaling) |
| <kbd>CTRL</kbd> + <kbd>R</kbd> | Show/hide grid lines |
| <kbd>CTRL</kbd> + <kbd>L</kbd> | Show/hide axis legends |
| <kbd>N</kbd> | Intensity mode: Normal |
| <kbd>P</kbd> | Intensity mode: Percentage |
| <kbd>S</kbd> | Intensity mode: Snam-to-maximum |
| <kbd>I</kbd> | 1D draw mode: peaks |
| <kbd>R</kbd> | 1D draw mode: raw data |
| <kbd>CTRL</kbd> + <kbd>ALT</kbd> + <kbd>Home</kbd> | 2D draw mode: increase minimum canvas coverage threshold (for raw peak scaling)|
| <kbd>CTRL</kbd> + <kbd>ALT</kbd> + <kbd>End</kbd> | 2D draw mode: decrease minimum canvas coverage threshold (for raw peak scaling) |
| <kbd>CTRL</kbd> + <kbd>ALT</kbd> + <kbd>+</kbd> | 2D draw mode: increase maximum point size (for raw peak scaling) |
| <kbd>CTRL</kbd> + <kbd>ALT</kbd> + <kbd>-</kbd> | 2D draw mode: decrease maximum point size (for raw peak scaling) |

> **_NOTE:_** `Home` on macOS keyboards is also `Fn`+`ArrowLeft`. `End` on macOSX keyboards is also `Fn`+`ArrowRight`.
> **_NOTE:_** <kbd>Home</kbd> on macOS keyboards is also <kbd>Fn</kbd> + <kbd>ArrowLeft</kbd>. <kbd>End</kbd> on macOSX keyboards is also <kbd>Fn</kbd> + <kbd>ArrowRight</kbd>.

## Annotations in 1D view

| Hotkey | Function |
|----------------------|-----------------------------------------------------|
| `CTRL`+`A` | Select all annotations of the current layer |
| `DEL` | Delete all currently selected annotations |
| <kbd>CTRL</kbd> + <kbd>A</kbd> | Select all annotations of the current layer |
| <kbd>DEL</kbd> | Delete all currently selected annotations |

## Advanced

| Hotkey | Function |
|----------------------|-----------------------------------------------------|
| `CTRL`+`T` | Apply TOPP tool to the current layer |
| `CTRL`+`SHIFT`+`T` | Apply TOPP tool to the visible data of the current layer|
| `F4` | Re-run TOPP tool |
| `CTRL` + `M` | Show layer meta information |
| `CTRL` + `I` | Annotate with identification results |
| `1` | Show precursor peaks (2D peak layer) |
| `2` | Show projections (2D peak layer) |
| `5` | Show overall convex hull (2D feature layer) |
| `6` | Show all convex hulls (2D feature layer) |
| `7` | Show numbers and labels (2D feature layer) |
| `9` | Show consensus elements (2D consensus layer) |
| <kbd>CTRL</kbd> + <kbd>T</kbd> | Apply TOPP tool to the current layer |
| <kbd>CTRL</kbd> + <kbd>SHIFT</kbd> + <kbd>T</kbd> | Apply TOPP tool to the visible data of the current layer|
| <kbd>F4</kbd> | Re-run TOPP tool |
| <kbd>CTRL</kbd> + <kbd>M</kbd> | Show layer meta information |
| <kbd>CTRL</kbd> + <kbd>I</kbd> | Annotate with identification results |
| <kbd>1</kbd> | Show precursor peaks (2D peak layer) |
| <kbd>2</kbd> | Show projections (2D peak layer) |
| <kbd>5</kbd> | Show overall convex hull (2D feature layer) |
| <kbd>6</kbd> | Show all convex hulls (2D feature layer) |
| <kbd>7</kbd> | Show numbers and labels (2D feature layer) |
| <kbd>9</kbd> | Show consensus elements (2D consensus layer) |

## Help


| Hotkey | Function |
|----------------------|-----------------------------------------------------|
| `F1` | Show TOPPView online tutorial |
| `SHIFT` + `F1` | Activate *What's this?* mode |
| <kbd>F1</kbd> | Show TOPPView online tutorial |
| <kbd>SHIFT</kbd> + <kbd>F1</kbd> | Activate *What's this?* mode |
2 changes: 1 addition & 1 deletion docs/tutorials/TOPP/quality-control.md
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Expand Up @@ -182,7 +182,7 @@ raw mzML file

### TopNoverRT

The TopNoverRT metric calculates the ScanEventNumber (number of the MS2 scans after the MS1 scan) and adds them as the
The **TopNoverRT** metric calculates the ScanEventNumber (number of the MS2 scans after the MS1 scan) and adds them as the
new metavalue `ScanEventNumber` to the PeptideIdentifications. It finds all unidentified MS2-Spectra and adds corresponding
`empty` PeptideIdentifications without sequence as placeholders to the unassigned PeptideIdentification list.
Furthermore, it adds the metavalue `identified` to the PeptideIdentification.
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14 changes: 7 additions & 7 deletions docs/tutorials/TOPP/views-in-toppview.md
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Expand Up @@ -13,19 +13,19 @@ and one for measuring:
- It is activated by default
- Move the mouse while holding the mouse button down to translate the current view
- Arrow keys can be used to translate the view without entering translate mode (in 1D-View you can additionally
use `Shift`-key to jump to the next peak)
use <kbd>Shift</kbd> to jump to the next peak)
- Zoom mode
- All previous zoom levels are stored in a zoom history. The zoom history can be traversed using `CTRL+`/`CTRL-` or the
- All previous zoom levels are stored in a zoom history. The zoom history can be traversed using <kbd>CTRL</kbd> + <kbd>+</kbd>/<kbd>CTRL</kbd> + <kbd>-</kbd> or the
mouse wheel (scroll up and down)
- Zooming into the data:
- Mark an area in the current view with your mouse, while holding the left mouse button plus the `CTRL` key to zoom
- Mark an area in the current view with your mouse, while holding the left mouse button plus the <kbd>CTRL</kbd> key to zoom
to this area.
- You can also use your mouse wheel to traverse the zoom history.
- If you have reached the end of the history, keep on pressing `CTRL+` or scroll up, the current area will be
- If you have reached the end of the history, keep on pressing <kbd>CTRL</kbd> + <kbd>+</kbd> or scroll up, the current area will be
enlarged by a factor of `1.25`.
- Pressing the `Backspace` key resets the zoom and zoom history.
- Pressing <kbd>Backspace</kbd> resets the zoom and zoom history.
- Measure mode
- It is activated using the `SHIFT` key
- It is activated using <kbd>SHIFT</kbd>.
- Press the left mouse button down while a peak is selected and drag the mouse to another peak to measure the
distance between peaks.
- This mode is implemented in the 1D and 2D mode.
Expand All @@ -49,7 +49,7 @@ between abundant peaks have been measured and subsequently replaced by their cor
This is done by right-clicking a distance annotation and selecting **Edit** from the context menu. Additionally, peak
annotations and text labels have been added by right-clicking peaks and selecting **Add peak** annotation or by right
clicking anywhere and selecting **Add Label**, respectively. Multiple annotations can be selected by holding down the
`CTRL` key while clicking them. They can be moved around by dragging the mouse and deleted by pressing `DEL`.
<kbd>CTRL</kbd> key while clicking them. They can be moved around by dragging the mouse and deleted by pressing <kbd>DEL</kbd>.

![TOPPView 1D](../../images/tutorials/topp/TOPPView_1D.png)

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3 changes: 1 addition & 2 deletions docs/tutorials/TOPPAS/examples.md
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Expand Up @@ -2,8 +2,7 @@ Examples
========

The following sections explain the example pipelines TOPPAS comes with. Open them by selecting **File** > **Open example file**.
All input files and parameters are already specified, so you can just hit **Pipeline** > **Run** (or press `F5`) and see what
happens.
All input files and parameters are already specified, so you can just hit **Pipeline** > **Run** (or press <kbd>F5</kbd>) and see what happens.

## Profile data processing

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2 changes: 1 addition & 1 deletion docs/tutorials/TOPPAS/general-introduction.md
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Expand Up @@ -14,7 +14,7 @@ The following figure shows a simple example pipeline that has just been created
To create a new TOPPAS file, do any of the following:

- Open TOPPAS without providing any existing workflow - an empty workflow will be opened automatically.
- In a running TOPPAS program, choose: **File** > **New**
- In a running TOPPAS program, choose: **File** > **New**.
- Create an empty file in your file browser (explorer) with the suffix `.toppas` and double-click it (on Windows systems
all `.toppas` files are associated with TOPPAS automatically during installation of OpenMS, on Linux, and macOS you
might need to manually associate the extension).
44 changes: 22 additions & 22 deletions docs/tutorials/TOPPAS/user-interface.md
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Expand Up @@ -19,7 +19,7 @@ workflow, or if it just would not make sense, e.g. if its target is an input fil
file node (#1) and the OMSSAAdapter (#5) tool is painted yellow which indicates it is not ready yet, because no input
files have been specified.

![TOPPAS Edges](../../images/tutorials/TOPPAS_edges.png)
![TOPPAS Edges](../../images/tutorials/toppas/TOPPAS_edges.png)

The input/output mapping of connections can be changed at any time during the editing process by double-clicking an
connections or by selecting **Edit I/O mapping** from the context menu which appears when a connection is right-clicked.
Expand All @@ -30,21 +30,21 @@ The following figure shows a possible next step: the user has double-clicked one
its parameters. By default, the standard parameters are used for each tool. Again, this can also be done by selecting
**Edit parameters** from the context menu of the tool.

![TOPPAS Parameters](../../images/tutorials/TOPPAS_parameters.png)
![TOPPAS Parameters](../../images/tutorials/toppas/TOPPAS_parameters.png)

Once the pipeline has been set up, specify the input files before executing the pipeline. This is done by double-clicking
Once the pipeline has been set up, specify the input files before executing the pipeline. This is done by double-clicking
an input node and selecting the desired files in the dialog that appears. Input nodes have a special mode named
**recycling mode**, i.e., if the input node has fewer files than the following node has rounds (as it might have two
incoming connections) then the files are recycled until all rounds are satisfied. This might be useful if one input node
specifies a single database file (for a Search-Adapter like Mascot) and another input node has the actual MS2 experiments
(which is usually more than one). Then the database input node would be set to `recycle` the database file, i.e. use it for
every run of the MascotAdapter node. The input list can be recycled an arbitrary number of times, but the recycling has to be
`complete`, i.e. the number of rounds of the downstream node have to be a multiple of the number of input files. Recycling mode
can be activated by right-clicking the input node and selecting the according entry from the context menu. Finally, if you have
input and output nodes at every end of your pipeline and all connections are green, select **Pipeline** > **Run** in the menu
bar or just press `F5`.

![TOPPAS Run Options](../../images/tutorials/TOPPAS_run_options.png)
**recycling mode**, i.e., if the input node has fewer files than the following node has rounds (as it might have two incoming
connections) then the files are recycled until all rounds are satisfied. This might be useful if one input node specifies a
single database file (for a Search-Adapter like Mascot) and another input node has the actual MS2 experiments (which is
usually more than one). Then the database input node would be set to `recycle` the database file, i.e. use it for every run of
the MascotAdapter node. The input list can be recycled an arbitrary number of times, but the recycling has to be `complete`,
i.e. the number of rounds of the downstream node have to be a multiple of the number of input files. Recycling mode can be
activated by right-clicking the input node and selecting the according entry from the context menu. Finally, if you have input
and output nodes at every end of your pipeline and all connections are green, select **Pipeline** > **Run** in the menu bar or
just press <kbd>F5</kbd>.

![TOPPAS Run Options](../../images/tutorials/toppas/TOPPAS_run_options.png)

When asked for an output file directory `TOPPAS_out` as sub-directory, will be created. This directory will
contain the output files. Specify the number of jobs TOPPAS is allowed to run in parallel. If a number greater than 1 is
Expand Down Expand Up @@ -76,8 +76,8 @@ Using the mouse:

- drag and drop tools from the TOPP tool list onto the workflow window (you can also double-click them instead)
- select items (by clicking)
- select multiple items (by holding down `CTRL` while clicking)
- select multiple items (by holding down `CTRL` and dragging the mouse in order to "catch" items with a selection
- select multiple items (by holding down <kbd>CTRL</kbd> while clicking)
- select multiple items (by holding down <kbd>CTRL</kbd> and dragging the mouse in order to "catch" items with a selection
rectangle)
- move all selected items (by dragging one of them)
- draw a new connection from one node to another (by dragging; source must be deselected first)
Expand All @@ -90,15 +90,15 @@ Using the mouse:

Using the keyboard:

- delete all selected items (`DEL` or `BACKSPACE`)
- zoom in and out (`+`/`-`)
- run the pipeline (`F5`)
- open this tutorial (`F1`)
- delete all selected items (<kbd>DEL</kbd> or <kbd>BACKSPACE</kbd>)
- zoom in and out (<kbd>+</kbd> / <kbd>-</kbd>)
- run the pipeline (<kbd>F5</kbd>)
- open this tutorial (<kbd>F1</kbd>)

Using the mouse` + `keyboard:
Using the mouse + keyboard:

- copy a node's parameters to another node (only parameters with identical names will be copied, e.g.,
`fixed_modifications`) (`CTRL` while creating an edge) The edge will be colored as dark magenta to indicate parameter
`fixed_modifications`) (<kbd>CTRL</kbd> while creating an edge) The edge will be colored as dark magenta to indicate parameter
copying.

## Menus
Expand Down