diff --git a/docs/topp/ini-file-editor.md b/docs/topp/ini-file-editor.md index 6012e92c..541316c1 100644 --- a/docs/topp/ini-file-editor.md +++ b/docs/topp/ini-file-editor.md @@ -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 F2. The documentation of each value is shown in the text area on the bottom of the widget. diff --git a/docs/tutorials/TOPP/data-editing-in-toppview.md b/docs/tutorials/TOPP/data-editing-in-toppview.md index 1c6fe80a..ac1925c1 100644 --- a/docs/tutorials/TOPP/data-editing-in-toppview.md +++ b/docs/tutorials/TOPP/data-editing-in-toppview.md @@ -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 DEL key. diff --git a/docs/tutorials/TOPP/hotkeys-table.md b/docs/tutorials/TOPP/hotkeys-table.md index a60d1339..df14769d 100644 --- a/docs/tutorials/TOPP/hotkeys-table.md +++ b/docs/tutorials/TOPP/hotkeys-table.md @@ -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 | +| CTRL + O | Open file | +| CTRL + W | Close current window | +| CTRL + S | Save current layer | +| CTRL + SHIFT + S | 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 | +| 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 | | Mouse wheel | Move up and down in zoom history | -| `CTRL+G` | Goto dialog | -| `Backspace` | Reset zoom | -| `PageUp` | Select previous layer | -| `PageDown` | Select next layer | +| CTRL + G | Go to dialog | +| Backspace | Reset zoom | +| PageUp | Select previous layer | +| PageDown | 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) | +| CTRL + R | Show/hide grid lines | +| CTRL + L | Show/hide axis legends | +| N | Intensity mode: Normal | +| P | Intensity mode: Percentage | +| 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) | -> **_NOTE:_** `Home` on macOS keyboards is also `Fn`+`ArrowLeft`. `End` on macOSX keyboards is also `Fn`+`ArrowRight`. +> **_NOTE:_** Home on macOS keyboards is also Fn + ArrowLeft. End on macOSX keyboards is also Fn + ArrowRight. ## Annotations in 1D view | Hotkey | Function | |----------------------|-----------------------------------------------------| -| `CTRL`+`A` | Select all annotations of the current layer | -| `DEL` | Delete all currently selected annotations | +| CTRL + A | Select all annotations of the current layer | +| DEL | 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) | +| 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) | ## Help | Hotkey | Function | |----------------------|-----------------------------------------------------| -| `F1` | Show TOPPView online tutorial | -| `SHIFT` + `F1` | Activate *What's this?* mode | +| F1 | Show TOPPView online tutorial | +| SHIFT + F1 | Activate *What's this?* mode | diff --git a/docs/tutorials/TOPP/quality-control.md b/docs/tutorials/TOPP/quality-control.md index ce539273..1ffd78b7 100644 --- a/docs/tutorials/TOPP/quality-control.md +++ b/docs/tutorials/TOPP/quality-control.md @@ -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. diff --git a/docs/tutorials/TOPP/views-in-toppview.md b/docs/tutorials/TOPP/views-in-toppview.md index 63b9eb98..c1db0b64 100644 --- a/docs/tutorials/TOPP/views-in-toppview.md +++ b/docs/tutorials/TOPP/views-in-toppview.md @@ -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 Shift 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 CTRL + +/CTRL + - 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 CTRL 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 CTRL + + 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 Backspace resets the zoom and zoom history. - Measure mode - - It is activated using the `SHIFT` key + - It is activated using SHIFT. - 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. @@ -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`. +CTRL key while clicking them. They can be moved around by dragging the mouse and deleted by pressing DEL. ![TOPPView 1D](../../images/tutorials/topp/TOPPView_1D.png) diff --git a/docs/tutorials/TOPPAS/examples.md b/docs/tutorials/TOPPAS/examples.md index 127768cd..e9c129ec 100644 --- a/docs/tutorials/TOPPAS/examples.md +++ b/docs/tutorials/TOPPAS/examples.md @@ -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 F5) and see what happens. ## Profile data processing diff --git a/docs/tutorials/TOPPAS/general-introduction.md b/docs/tutorials/TOPPAS/general-introduction.md index 5a0b44d2..afd02cf2 100644 --- a/docs/tutorials/TOPPAS/general-introduction.md +++ b/docs/tutorials/TOPPAS/general-introduction.md @@ -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). diff --git a/docs/tutorials/TOPPAS/user-interface.md b/docs/tutorials/TOPPAS/user-interface.md index c96d55ed..68702578 100644 --- a/docs/tutorials/TOPPAS/user-interface.md +++ b/docs/tutorials/TOPPAS/user-interface.md @@ -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. @@ -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 F5. + +![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 @@ -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 CTRL while clicking) +- select multiple items (by holding down CTRL 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) @@ -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 (DEL or BACKSPACE) +- zoom in and out (+ / -) +- run the pipeline (F5) +- open this tutorial (F1) -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`) (CTRL while creating an edge) The edge will be colored as dark magenta to indicate parameter copying. ## Menus