Updating to v1.2.1.4

lukasz-migas · Jan 9, 2019 · a24adaf · a24adaf
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diff --git a/ORIGAMI_ANALYSE/img/added.png b/ORIGAMI_ANALYSE/img/added.png
diff --git a/ORIGAMI_ANALYSE/img/changed.png b/ORIGAMI_ANALYSE/img/changed.png
diff --git a/ORIGAMI_ANALYSE/img/fixed.png b/ORIGAMI_ANALYSE/img/fixed.png
diff --git a/ORIGAMI_ANALYSE/img/improved.png b/ORIGAMI_ANALYSE/img/improved.png
diff --git a/ORIGAMI_ANALYSE/origami/ORIGAMI.spec b/ORIGAMI_ANALYSE/origami/ORIGAMI.spec
@@ -38,7 +38,7 @@ block_cipher = None
 # pyinstaller ORIGAMI.spec -y --clean
 
 # Set version number
-version = "1.2.1.3"
+version = "1.2.1.4"
 
 current_dir = os.getcwd()
 origami_dir_name = "ORIGAMI_v{}".format(version)

diff --git a/ORIGAMI_ANALYSE/v1.2.1.4/annotated_spectrum.png b/ORIGAMI_ANALYSE/v1.2.1.4/annotated_spectrum.png
diff --git a/ORIGAMI_ANALYSE/v1.2.1.4/interactive_copy_style.png b/ORIGAMI_ANALYSE/v1.2.1.4/interactive_copy_style.png
diff --git a/ORIGAMI_ANALYSE/v1.2.1.4/interactive_customise_item.png b/ORIGAMI_ANALYSE/v1.2.1.4/interactive_customise_item.png
diff --git a/ORIGAMI_ANALYSE/v1.2.1.4/interactive_label_movement.gif b/ORIGAMI_ANALYSE/v1.2.1.4/interactive_label_movement.gif
diff --git a/ORIGAMI_ANALYSE/v1.2.1.4/msms_panel.png b/ORIGAMI_ANALYSE/v1.2.1.4/msms_panel.png
diff --git a/ORIGAMI_ANALYSE/v1.2.1.4/msms_settings.png b/ORIGAMI_ANALYSE/v1.2.1.4/msms_settings.png
diff --git a/...I_TUTORIALS/Document_files/TUTORIAL_Open_analyse_ORIGAMI-MS_files/ORIGAMI_ConA_z20.pickle b/...I_TUTORIALS/Document_files/TUTORIAL_Open_analyse_ORIGAMI-MS_files/ORIGAMI_ConA_z20.pickle
diff --git a/...ALS/Document_files/TUTORIAL_Open_analyse_ORIGAMI-MS_files/comparison_document_ConA.pickle b/...ALS/Document_files/TUTORIAL_Open_analyse_ORIGAMI-MS_files/comparison_document_ConA.pickle
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -55,7 +55,7 @@ nav:
         - 'CCS compendium': interactive-examples/ccs-compendium.md
         - 'Proteomics - MS/MS': interactive-examples/protemics-scans.md
     - Changelog: 
-        - 'v1.2.1.1 - 27/12/2018': changelog/v1.2.1.1-27-12-2018.md
+        - 'v1.2.1.1 - 27/12/2018': changelog/v1.2.1.4-9-1-2019.md
         - 'v1.2.0.3 - 7/11/2018': changelog/v1.2.0.3-5-11-2018.md
     - Request New Features: main/request.md
     - Report Bugs: main/bugs.md

diff --git a/site-source/changelog/img/v1.2.1.4-9-1-2019/annotated_spectrum.png b/site-source/changelog/img/v1.2.1.4-9-1-2019/annotated_spectrum.png
diff --git a/site-source/changelog/img/v1.2.1.4-9-1-2019/interactive_copy_style.png b/site-source/changelog/img/v1.2.1.4-9-1-2019/interactive_copy_style.png
diff --git a/site-source/changelog/img/v1.2.1.4-9-1-2019/interactive_customise_item.png b/site-source/changelog/img/v1.2.1.4-9-1-2019/interactive_customise_item.png
diff --git a/site-source/changelog/img/v1.2.1.4-9-1-2019/interactive_label_movement.gif b/site-source/changelog/img/v1.2.1.4-9-1-2019/interactive_label_movement.gif
diff --git a/site-source/changelog/img/v1.2.1.4-9-1-2019/msms_panel.png b/site-source/changelog/img/v1.2.1.4-9-1-2019/msms_panel.png
diff --git a/site-source/changelog/img/v1.2.1.4-9-1-2019/msms_settings.png b/site-source/changelog/img/v1.2.1.4-9-1-2019/msms_settings.png
diff --git a/site-source/changelog/v1.2.1.1-27-12-2018.md → site-source/changelog/v1.2.1.4-9-1-2019.md b/site-source/changelog/v1.2.1.1-27-12-2018.md → site-source/changelog/v1.2.1.4-9-1-2019.md
@@ -43,7 +43,7 @@
 ## Interactive panel
 
 ![Added](img/added.png) Made big progres in terms of copying/applying styles for plot elements. When you
-double-click on any element in the file list a new window will appear where you can individually adjust plot parameters. When you finished, you can right-click on that same (or any other) item in the list and select 'Copy style..'.  You can then select any other item in the list, right-click on it and select 'Apply style..'.
+double-click on any element in the file list a new window will appear where you can individually adjust plot parameters. When you finished, you can right-click on that same (or any other) item in the list and select 'Copy style..'. You can then select any other item in the list, right-click on it and select 'Apply style..'.
 
 ![Added](img/added.png) certain plot types (v-bar, h-bar, scatter, waterfall, multi-line/overlay) will now support addition of annotations (and their widgets). Annotations can correspond to anything you wish to say about specific region of a dataset.
 
@@ -76,7 +76,7 @@ double-click on any element in the file list a new window will appear where you
 
 ![Added](img/added.png) MS/MS files can now be exported in an interactive format (.html document). This feature is still in development and I imagine will not be stable until v1.2.2 at the earliest. At the moment, individual scans of MS/MS file (.mgf only) can be annotated (e.g. fragments can be generated) and added to the file. Scans that have been user-annotated can be subsequently exported. This will be properly showcased in a tutorial.
 
-![Added](img/added.png) Added two new options in the **Action menu** which permit improved population of the table by either exlcuding scans with PTMs and excluding scans without identification. Clicking on either of these will automatically trigger re-population of the table based on the selected options.
+![Added](img/added.png) Added two new options in the **Action menu** which permit improved population of the table by either excluding scans with PTMs and excluding scans without identification. Clicking on either of these will automatically trigger re-population of the table based on the selected options.
 
 ![Added](img/added.png) You can see what PTMs have been included in the scan by clicking on the **Modifications list**
 
@@ -92,10 +92,38 @@ double-click on any element in the file list a new window will appear where you
 
 ![Fixed](img/fixed.png) When selecting frag-all option, appropriate checkboxes will be ticked from now on
 
+![Fixed](img/fixed.png) Fixed fragment generator to stop overriding fragments with same name (e.g. y1+ was equal y_H2Ox11+...)
+
 ## Other data -> Annotated data
 
 ![Added](img/added.png) Added new keyword 'axis_url'/'axis_urls' to the data parser. These keywords can be used to provide web addresses which can be attached to the data (scatter points only for now). If valid URL address is provided, when you tap on a point you will be taken to a new tab in your browser which corresponds to the web address. This is only valid in the interactive plots
 
 ![Changed](img/changed.png) Changed the poorly selected name of 'Other data' to 'Annotated data'
 
 ## Figures
+
+Updated MS/MS panel
+
+![MSMS](img/v1.2.1.4-9-1-2019/interactive_customise_item.png)
+
+MS/MS customisation window
+
+![MSMS](img/v1.2.1.4-9-1-2019/msms_settings.png)
+
+Annotated MS/MS mass spectrum with automatically generated arrows
+
+![MSMS](img/v1.2.1.4-9-1-2019/annotated_spectrum.png)
+
+Interactive data customisation window
+
+![Interactive](img/v1.2.1.4-9-1-2019/interactive_customise_item.png)
+
+Interactive copy style
+
+![Interactive](img/v1.2.1.4-9-1-2019/interactive_copy_style.png)
+
+## Animation
+
+Interactive adjustment of labels
+
+![Interactive](img/v1.2.1.4-9-1-2019/interactive_label_movement.gif)