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index.html

@@ -477,7 +477,9 @@ <h1 id="dbverse"><code>dbverse</code></h1>
 <!-- badges: start -->
 
 <p><a href="https://lifecycle.r-lib.org/articles/stages.html#experimental"><img alt="Lifecycle:
-experimental" src="https://img.shields.io/badge/lifecycle-experimental-orange.svg" /></a></p>
+experimental" src="https://img.shields.io/badge/lifecycle-experimental-orange.svg" /></a>
+<a href="conduct/"><img alt="Contributor
+Covenant" src="https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg" /></a></p>
 <!-- badges: end -->
 
 <p>**Note: work in progress **</p>

overview/index.html

@@ -259,97 +259,96 @@ <h2 id="class-diagram">Class Diagram</h2>
 <div class="mermaid">classDiagram
 direction LR
 
-namespace Data {
-
-    class tabular{
+namespace Input_Data {
+    class numerical{
         .mtx
         .csv
         .parquet
-        dgCMatrix
-        data.frames
+        dgcMatrix
+        matrix
+        data.frame
+        data.table
     }
 
     class geometries{
-        .shp
-        .geojson
+        50+ spatial file formats
         sf::sf
         terra::spatVector
     }
 
+    class sequences{
+        10+ genomic file formats
+    }
 }
 
-namespace dbverse {
+namespace computer {
+    class database
+}
 
+namespace dbverse {
     class dbMatrix_lib{
-
+        class dbMatrix
     }
 
     class dbSpatial_lib{
+        class dbSpatial
+    }
 
+    class dbSequence_lib{
+        class dbSequence
     }
 
     class dbData_lib{
-
+        class dbData
     }
-
 }
 
-namespace dbData_lib {
-    class dbData {
-        &lt;&lt;base virtual class&gt;&gt;
-        + value: duckdb_table
-        + name: character string
-        + init: boolean
-        - DBI::*()
+namespace dbMatrix_lib {
+    class dbMatrix {
+        + dbData: dbData
+        + dim_names: [enum,enum]
+        + dims: [int, int]
+        + class: "dbSparseMatrix" | "dbDenseMatrix"
+        - Arith
+        - Ops
+        - matrix summary functions()
     }
-
 }
 
 namespace dbSpatial_lib {
-
     class dbSpatial{
-    - ST_*(geom) [DuckDB_spatial]
-    }
-
-    class dbSpatialPoints{
-    - ST_*(geom_point) 
-    }
-
-    class dbSpatialPolygons{
-    - ST_*(geom_polygon)
+        + dbData: dbData
+        - ST_*(geom) [DuckDB Spatial Extension]
     }
 }
 
-namespace dbMatrix_lib {
-    class dbMatrix {
-        + dim_names: [enum,enum]
-        + dims: [int, int]
-        + class: "sparse" | "dense"
-        - dbMatrix::*()
-        - dbMatrixStats::*()
+namespace dbSequence_lib {
+    class dbSequence{
+        + dbData: dbData
     }
+}
 
-    class dbSparseMatrix{
-
-    }
-
-    class dbDenseMatrix{
-
+namespace dbData_lib {
+    class dbData {
+        &lt;&lt;base virtual class&gt;&gt;
+        + value: Input_Data
+        + name: table_name
+        + init: boolean
+        + conn: DuckDB connection
+        - DBI::()
+        - dplyr::()
     }
 }
 
+numerical &lt;..&gt; dbMatrix_lib : read/write
+geometries &lt;..&gt; dbSpatial_lib : read/write
+sequences &lt;..&gt; dbSequence_lib : read/write
 
-tabular &lt;..&gt; dbData_lib : read/write
-geometries &lt;..&gt; dbData_lib : read/write
-
-dbData_lib --&gt; dbMatrix_lib
-dbData_lib --&gt; dbSpatial_lib
-
-dbSpatial --&gt; dbSpatialPoints
-dbSpatial --&gt; dbSpatialPolygons
+dbMatrix_lib --&gt; dbData_lib
+dbSpatial_lib --&gt; dbData_lib
+dbSequence_lib --&gt; dbData_lib
 
-dbMatrix --&gt; dbDenseMatrix
-dbMatrix --&gt; dbSparseMatrix
+dbData_lib &lt;..&gt; database : connect/disconnect/cache
 </div>
 </article>
 </div>