https://sourceforge.net/p/atomprobelab/wiki/overlapProblemBuilder/Recent changes to overlapProblemBuilderenWed, 28 Mar 2018 16:25:04 -0000https://sourceforge.net/p/atomprobelab/wiki/overlapProblemBuilder/<div class="markdown_content"><pre>--- v2 +++ v3 @@ -62,7 +62,7 @@ rangeElements = The element names which are in the ranges table - ##Notes + ## Notes ---- * Named ions are ignored * Minimum abundance is in %, so 0.21 = 0.21% </pre> </div>A LondonWed, 28 Mar 2018 16:25:04 -0000https://sourceforge.net1a191180583b87f8fe855a60730593052471434fhttps://sourceforge.net/p/atomprobelab/wiki/overlapProblemBuilder/<div class="markdown_content"><pre>--- v1 +++ v2 @@ -1,11 +1,14 @@ #overlapProblemBuilder +----- ####Build an overlap problem struct ## Syntax +---- overlapProblem = overlapProblemBuilder(varargin) Takes a name-parameter list and build an overlapProblem struct which can be used in other problem-solving functions ## Inputs +---- Inputs are given by the name-value pairs defined below. 'rangeFile' Rrng file or range cell array (see rangeReaderCell) 'ions' List of ions in the ion-cell array format @@ -41,7 +44,7 @@ 'rangeStart',r1,'rangeEnd',r2) ##Outputs - +---- overlapProblem is a struct (structure) containing the following named values. They can be accessed by overlapProblem."name" where "name" is: overlapIons = each cell contains a cell array of ions @@ -60,7 +63,7 @@ ##Notes - +---- * Named ions are ignored * Minimum abundance is in %, so 0.21 = 0.21% * The default minimum abundance is set at 0.21% so that O-18 is </pre> </div>A LondonWed, 28 Mar 2018 16:24:43 -0000https://sourceforge.net35fda9902bd7d7e4b65595682fb8a4eb72f79416https://sourceforge.net/p/atomprobelab/wiki/overlapProblemBuilder/<div class="markdown_content"><h1 id="overlapproblembuilder">overlapProblemBuilder</h1> <h4 id="build-an-overlap-problem-struct">Build an overlap problem struct</h4> <h2 id="syntax">Syntax</h2> <p>overlapProblem = overlapProblemBuilder(varargin)</p> <p>Takes a name-parameter list and build an overlapProblem struct which can be used in other problem-solving functions</p> <h2 id="inputs">Inputs</h2> <p>Inputs are given by the name-value pairs defined below. <br/> 'rangeFile' Rrng file or range cell array (see rangeReaderCell)<br/> 'ions' List of ions in the ion-cell array format<br/> 'minAbundance' Minimum peak abundance in %<br/> 'rangeStart' Pre-peak range scale which is multiplied by sqrt(peak Da)<br/> 'rangeEnd' Post-peak range scale which is multiplied by sqrt(peak Da)<br/> 'adIons' Additional ions to add (in cell-array format, see notes*)</p> <p>An overlap problem can be defined in two ways:<br/> (1) Using the ranges defined in a range file<br/> (2) Using a finite width of m/z peaks</p> <p>Example (1)a: Using ranges with the ions as defined in the range file<br/> Use a range file "myRanges.rrng" with the default minimum abundance<br/> limit. The ions are built using the ranges given.<br/> overlapProblem = overlapProblemBuilder('rangeFile','myRanges.rrng')</p> <p>Example (1)b: Using ranges with different ions specified<br/> Use a range file "myRanges.rrng" with the default minimum abundance<br/> limit. The ions as defined by the list in "myIonsList"<br/> myIonsList = {{2,'Ti','O'},{1,'O',2}};<br/> overlapProblem = ...<br/> overlapProblemBuilder('rangeFile','myRanges.rrng','ions',myIonsList)</p> <p>Example (2): Use a list of ions and peak widths<br/> The ions are defined by the list in "myIonsList". The range widths are<br/> given by rs and rf.<br/> myIonsList = {{2,'Ti','O'},{1,'O',2}};<br/> r1 = 0.01;<br/> r2 = 0.02;<br/> overlapProblem = ...<br/> overlapProblemBuilder('ions',myIonsList,...<br/> 'rangeStart',r1,'rangeEnd',r2)</p> <h2 id="outputs">Outputs</h2> <p>overlapProblem is a struct (structure) containing the following named<br/> values. They can be accessed by overlapProblem."name" where "name" is:<br/> overlapIons = each cell contains a cell array of ions <br/> (cell) which are one overlap group<br/> overlapTable = A range centre-by-ions abundance table for <br/> each overlap group<br/> ionIndex = Which index in the ions list each ion in each <br/> overlap group is<br/> overlapIonNames = Which index in the ions list each ion in <br/> each overlap group is<br/> ions = Total list of all ions<br/> ionNames = Total list of all ion names with chrage states, <br/> e.g. Fe2O++<br/> ranges = m/z range windows and an elemental table<br/> rangeElements = The element names which are in the ranges table</p> <p>##Notes</p> <ul> <li>Named ions are ignored</li> <li>Minimum abundance is in %, so 0.21 = 0.21%</li> <li>The default minimum abundance is set at 0.21% so that O-18 is<br/> excluded</li> <li>Range widths are given by a start (pre-peak width) and end<br/> (post-peak width) which has units of sqrt(Da). If rs= rf = 0.01 and <br/> the peak is at 30 Da, then the start is 30-sqrt(30)<em>0.01 and the <br/> finish is 30+sqrt(30)</em>0.01 = 29.945 to 30.055 Da<br/> This is so that the m/z ranges have fixed sizes in TOF space, but<br/> variable widths in m/z space.</li> <li>Ions specified by the adIons parameter should be in the cell array<br/> format, e.g. Ti2O++ would be {{2,'Ti',2,'O'}}. You can provide a list<br/> of ions like so: {{1,'Fe'},{2,'Fe'}, ... }.<br/> See ionStr2ions for futher information about the ion-cell format.</li> </ul></div>A LondonWed, 28 Mar 2018 16:23:05 -0000https://sourceforge.neta373f6bb5976caccadbaf487ba1f467575b9bf18