Proteins Window

The Proteins window shows each entry of a proteins database file. See the file formats page for details about this file. Each entry is shown in three parts:

  1. The primary protein symbol.
  2. The primary protein name.
  3. A list of secondary protein names. These are also known as 'aliases' for the protein, and may consist of other symbols or names for the protein, or for the genes associated with the protein.
Each of these information fields is editable, and the edited protein database may be written out to another file. Controls within the window allow you to navigate through the protein database, and to search for protein entries based on specific fields of the database. Searches of the protein database may also be performed from the Abstracts window.

Reading protein files

To read a proteins file, click the 'Read Proteins...' button. Navigate through the Mac file system using the Open dialog, and choose a file to read. The file will be read and parsed, and all protein entries stored in memory. Note that reading a proteins file will first erase any other protein entries already in memory.

Navigating through protein entries

Drag or click on the slider at the bottom of the window to continuously scroll through the entries in the proteins database. You can also go forward or backward by one entry at a time by clicking on the toggle switch at the lower right corner of the window.

Editing protein entries

The primary protein symbol, primary protein name, and list of secondary protein names are all editable. Changes made to these fields will not be written out to the proteins database file until you click the 'Write Proteins...' button. All seconday protein names begin with a '-' character, so that they can be distinguised from long lines that are wrapped by the text field. When the secondary names are entered into the database, the '-' and any leading spaces are stripped from each line. The '-' is added again when the names are displayed in the text field. You may either use a '-' or not when adding new entries to this field, but it will not appear in the database file.

Searching for proteins

To search for a string in the proteins database, type or paste text into the text field next to the 'Search For:' button, and then click the button. The three checkboxes control how the search is performed. You can search for strings in the primary protein symbol fields, the primary protein name fields, the secondary protein names fields, or any combination of the three. Click the 'Search For:' button to start searching from the beginning of the proteins database. Click the 'Next' button to repeat the search starting from the entry after the currently displayed entry. Any field of the database which is selected by the checkboxes and which contains the search string will trigger a match. Searches are case sensitive.

Selecting the font

To change the font of any of the protein text fields, click the mouse in the field and choose 'Select All' from the Edit menu. You can then access the Font menu and change the font with 'Show Fonts' or any of the other menu items. Only if you selected the entire text field will changes to the font persist to text in other protein entries.

Writing protein files

To write the current proteins database to a file, click the 'Write Proteins...' button. Navigate through the Mac file system using the Save dialog, and enter the name of a file to write. All entries for the current set of proteins will be written to the file. It is strongly recommended that you first make a copy of your existing proteins database file before overwriting it, as this operation cannot be undone.

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İSky Coyote 2002