Renamed ProteomeLayer.Intersection (from intersection) to follow Java class naming conventions

docs/source/user_guide/construct.rst

@@ -223,10 +223,10 @@ Relaxation
 """"""""""
 The ``relaxation`` parameter is a combination of four sub-parameters:
 ``intersection rate``, ``similarity threshold``, ``mcl inflation``
-and ``contrast``. The values for these parameter for each relaxation
-setting can be seen in the table below. We recommend using the
-``--relaxation`` option if there is any uncertainty about its
-sub-parameters.
+and ``contrast``. The values for these parameters for each relaxation
+setting can be seen in the table below. We strongly recommend using the
+``--relaxation`` option to control the grouping, but advanced users still
+have the option to control the individual sub-parameters.
 
 .. csv-table::
    :file: ../tables/relaxation.csv
@@ -286,8 +286,8 @@ Example commands
 
 .. code:: bash
 
-   $ pantools group tomato_DB
    $ pantools group -t=12 -r=4 tomato_DB
+   $ pantools group --intersection-rate=0.05 --similarity-threshold=65  --mcl-inflation=7.2 --contrast=5 tomato_DB
 
 Output
 """"""

src/main/java/nl/wur/bif/pantools/pangenome/ProteomeLayer.java

@@ -75,8 +75,8 @@ public class ProteomeLayer {
     private long[][] kmers_proteins_list;
     private int[] kmer_frequencies;
     private BlockingQueue<Node> proteins;
-    private BlockingQueue<intersection> intersections;
-    private BlockingQueue<intersection> similarities;
+    private BlockingQueue<nl.wur.bif.pantools.pangenome.ProteomeLayer.Intersection> intersections;
+    private BlockingQueue<nl.wur.bif.pantools.pangenome.ProteomeLayer.Intersection> similarities;
     private BlockingQueue<LinkedList> components; 
     private BlockingQueue<LinkedList> homology_groups_list; 
     private Node pangenome_node;
@@ -97,7 +97,7 @@ public class ProteomeLayer {
     /**
      * Implements the class for intersecting pair of proteins.
      */
-    public class intersection {
+    public class Intersection {
         public Node protein1;
         public Node protein2;
         public double similarity;
@@ -108,7 +108,7 @@ public class ProteomeLayer {
          * @param p2 The second protein.
          * @param s The normalized similarity score of two proteins
          */
-        public intersection(Node p1, Node p2, double s) {
+        public Intersection(Node p1, Node p2, double s) {
             protein1 = p1;
             protein2 = p2;
             similarity = s;
@@ -378,7 +378,7 @@ public class ProteomeLayer {
                                             crossing_protein = get_protein_sequence(crossing_protein_node);
                                             shorter_len = Math.min(protein_length, crossing_protein.length());
                                             if (counter >= frac * (shorter_len - PEPTIDE_SIZE + 1)) {
-                                                intersections.put(new intersection(protein_node, crossing_protein_node, 0));
+                                                intersections.put(new nl.wur.bif.pantools.pangenome.ProteomeLayer.Intersection(protein_node, crossing_protein_node, 0));
                                                 ++num_ins;
                                             }
                                         }
@@ -393,7 +393,7 @@ public class ProteomeLayer {
                                     crossing_protein = get_protein_sequence(crossing_protein_node);
                                     shorter_len = Math.min(protein_length, crossing_protein.length());
                                     if (counter >= frac * (shorter_len - PEPTIDE_SIZE + 1)) {
-                                        intersections.put(new intersection(protein_node, crossing_protein_node,0));
+                                        intersections.put(new nl.wur.bif.pantools.pangenome.ProteomeLayer.Intersection(protein_node, crossing_protein_node,0));
                                         ++num_ins;
                                     }
                                 }
@@ -408,7 +408,7 @@ public class ProteomeLayer {
                     System.out.print("0 ......................................... 100\n  "); 
                 // Signify the end of intersections queue.
                     for (i = 0; i < THREADS; ++i)
-                        intersections.put(new intersection(null, null,-1));// end of queue
+                        intersections.put(new nl.wur.bif.pantools.pangenome.ProteomeLayer.Intersection(null, null,-1));// end of queue
                 } catch(InterruptedException e) {
                     System.err.println(e.getMessage());
                 }
@@ -454,7 +454,7 @@ public class ProteomeLayer {
         public void run() {
             Node protein_node1, protein_node2;
             String protein1, protein2;
-            intersection ints;
+            nl.wur.bif.pantools.pangenome.ProteomeLayer.Intersection ints;
             int num_ints = 0;
             boolean all_intersections_found = false;
             int trsc = 0;
@@ -505,7 +505,7 @@ public class ProteomeLayer {
                 // Signify the end of the similarities queue.
                     //similarities.put(new intersection(null, null,0));
                     Node pangenome_node = GRAPH_DB.getNodeById(0);
-                    similarities.put(new intersection(pangenome_node, null, 0));
+                    similarities.put(new nl.wur.bif.pantools.pangenome.ProteomeLayer.Intersection(pangenome_node, null, 0));
                     tx.success();
                 } finally {
                     tx.close();
@@ -567,7 +567,7 @@ public class ProteomeLayer {
 
         @Override
         public void run() {
-            intersection ints;
+            nl.wur.bif.pantools.pangenome.ProteomeLayer.Intersection ints;
             int finished_thread_counter = 0;
             try{
                 ints = similarities.take();
@@ -577,7 +577,7 @@ public class ProteomeLayer {
                             if (ints.protein2 == null) {
                                 finished_thread_counter ++;
                                 if (finished_thread_counter == THREADS-2) {
-                                    similarities.put(new intersection(null, null, 0));
+                                    similarities.put(new nl.wur.bif.pantools.pangenome.ProteomeLayer.Intersection(null, null, 0));
                                 }
                                 ints = similarities.take();
                                 continue;