From ede468b3e5204537f77c738c064b5796c0fcaa35 Mon Sep 17 00:00:00 2001 From: greengypsy Date: Wed, 25 May 2022 16:26:51 +0930 Subject: [PATCH 1/2] added keyboard syntax plus other minor changes such as adding full stops to sentences --- docs/topp/ini-file-editor.md | 2 +- .../TOPP/data-editing-in-toppview.md | 2 +- docs/tutorials/TOPP/hotkeys-table.md | 80 +++++++++---------- docs/tutorials/TOPP/quality-control.md | 2 +- docs/tutorials/TOPP/views-in-toppview.md | 14 ++-- docs/tutorials/TOPPAS/examples.md | 3 +- docs/tutorials/TOPPAS/general-introduction.md | 2 +- docs/tutorials/TOPPAS/user-interface.md | 18 ++--- 8 files changed, 61 insertions(+), 62 deletions(-) diff --git a/docs/topp/ini-file-editor.md b/docs/topp/ini-file-editor.md index e5635936..81513618 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..5d272a6b 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 d4fca253..d57516b1 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 585624fd..0e070617 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. ![](../../images/tutorials/topp/TOPPView_1D.png) diff --git a/docs/tutorials/TOPPAS/examples.md b/docs/tutorials/TOPPAS/examples.md index 74fd1afd..6a0b9673 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 20d4bbad..285883c6 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 a5420377..b0e1e182 100644 --- a/docs/tutorials/TOPPAS/user-interface.md +++ b/docs/tutorials/TOPPAS/user-interface.md @@ -42,7 +42,7 @@ database file, i.e. use it for every run of the MascotAdapter node. The input li 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`. +connections are green, select **Pipeline** > **Run** in the menu bar or just press F5. ![](../../images/tutorials/TOPPAS_run_options.png) @@ -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 From ca8e5f2a94cc182fef3d383eb58ec587700108fc Mon Sep 17 00:00:00 2001 From: greengypsy Date: Wed, 25 May 2022 19:27:21 +0930 Subject: [PATCH 2/2] added spaces between symbols as discussed --- docs/tutorials/TOPP/hotkeys-table.md | 32 ++++++++++++------------ docs/tutorials/TOPP/views-in-toppview.md | 4 +-- docs/tutorials/TOPPAS/user-interface.md | 2 +- 3 files changed, 19 insertions(+), 19 deletions(-) diff --git a/docs/tutorials/TOPP/hotkeys-table.md b/docs/tutorials/TOPP/hotkeys-table.md index 5d272a6b..df14769d 100644 --- a/docs/tutorials/TOPP/hotkeys-table.md +++ b/docs/tutorials/TOPP/hotkeys-table.md @@ -5,10 +5,10 @@ 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 @@ -18,9 +18,9 @@ TOPPView Hotkeys | 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 + +,
CTRL + - | Move up and down in zoom history | | Mouse wheel | Move up and down in zoom history | -| CTRL+G | Go to dialog | +| CTRL + G | Go to dialog | | Backspace | Reset zoom | | PageUp | Select previous layer | | PageDown | Select next layer | @@ -29,33 +29,33 @@ TOPPView Hotkeys | Hotkey | Function | |----------------------|-----------------------------------------------------| -| CTRL+R | Show/hide grid lines | -| CTRL+L | Show/hide axis legends | +| 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) | +| 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 | +| 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| +| 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 | diff --git a/docs/tutorials/TOPP/views-in-toppview.md b/docs/tutorials/TOPP/views-in-toppview.md index 0e070617..f80bcb9e 100644 --- a/docs/tutorials/TOPP/views-in-toppview.md +++ b/docs/tutorials/TOPP/views-in-toppview.md @@ -15,13 +15,13 @@ and one for measuring: - Arrow keys can be used to translate the view without entering translate mode (in 1D-View you can additionally 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 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 Backspace resets the zoom and zoom history. - Measure mode diff --git a/docs/tutorials/TOPPAS/user-interface.md b/docs/tutorials/TOPPAS/user-interface.md index b0e1e182..54aa454d 100644 --- a/docs/tutorials/TOPPAS/user-interface.md +++ b/docs/tutorials/TOPPAS/user-interface.md @@ -91,7 +91,7 @@ Using the mouse: Using the keyboard: - delete all selected items (DEL or BACKSPACE) -- zoom in and out (+/-) +- zoom in and out (+ / -) - run the pipeline (F5) - open this tutorial (F1)