Rename "clustering" to "grouping"

MarWoes · Oct 9, 2017 · eba8d69 · eba8d69
1 parent 431eaed
commit eba8d69
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Showing 2 changed files with 6 additions and 6 deletions.
diff --git a/README.md b/README.md
@@ -38,7 +38,7 @@ These parameters are optional and may be omitted using the default values:
 
 | parameter | description | default value |
 |-------| ----------- |-----|
-| *enableClustering* | Group together calls with same chromosome values and similar breakpoint values | `true` |
+| *enableGrouping* | Group together calls with same chromosome values and similar breakpoint values | `true` |
 | *breakpointTolerance* | If grouping is enabled, this is the maximum distance where two breakpoints are considered similar. | `3` |
 | *csvDelimiter* | Character that delimits csv columns. | `";"` |
 | *collectionDelimiter* | A single cell in a csv table may have multiple values. These values are seperated by this character. |`","` |

diff --git a/src/main/java/de/imi/marw/viper/api/ViperServerConfig.java b/src/main/java/de/imi/marw/viper/api/ViperServerConfig.java
@@ -29,7 +29,7 @@ public class ViperServerConfig {
     private int igvPort = 9090;
     private char csvDelimiter = ';';
     private String collectionDelimiter = ",";
-    private boolean enableClustering = true;
+    private boolean enableGrouping = true;
     private int breakpointTolerance = 3;
     private String workDir = "/tmp/viper";
     private String fastaRef = "hg19";
@@ -201,16 +201,16 @@ public void setIgvMaxMemory(int igvMaxMemory) {
     }
 
     public boolean isClusteringEnabled() {
-        return enableClustering;
+        return enableGrouping;
     }
 
-    public void setEnableClustering(boolean enableClustering) {
-        this.enableClustering = enableClustering;
+    public void setEnableGrouping(boolean enableGrouping) {
+        this.enableGrouping = enableGrouping;
     }
 
     @Override
     public String toString() {
-        return "ViperServerConfig{" + "analysisFile=" + analysisFile + ", viperPort=" + viperPort + ", igvPort=" + igvPort + ", csvDelimiter=" + csvDelimiter + ", collectionDelimiter=" + collectionDelimiter + ", enableClustering=" + enableClustering + ", breakpointTolerance=" + breakpointTolerance + ", workDir=" + workDir + ", fastaRef=" + fastaRef + ", igvJar=" + igvJar + ", bamDir=" + bamDir + ", keepVcfSimple=" + keepVcfSimple + ", excludeRefVcfCalls=" + excludeRefVcfCalls + ", numPrecomputedSnapshots=" + numPrecomputedSnapshots + ", xslxExportWindowSize=" + xslxExportWindowSize + ", viewRange=" + viewRange + ", xvfbDisplay=" + xvfbDisplay + ", xvfbWidth=" + xvfbWidth + ", xvfbHeight=" + xvfbHeight + ", igvMaxMemory=" + igvMaxMemory + '}';
+        return "ViperServerConfig{" + "analysisFile=" + analysisFile + ", viperPort=" + viperPort + ", igvPort=" + igvPort + ", csvDelimiter=" + csvDelimiter + ", collectionDelimiter=" + collectionDelimiter + ", enableClustering=" + enableGrouping + ", breakpointTolerance=" + breakpointTolerance + ", workDir=" + workDir + ", fastaRef=" + fastaRef + ", igvJar=" + igvJar + ", bamDir=" + bamDir + ", keepVcfSimple=" + keepVcfSimple + ", excludeRefVcfCalls=" + excludeRefVcfCalls + ", numPrecomputedSnapshots=" + numPrecomputedSnapshots + ", xslxExportWindowSize=" + xslxExportWindowSize + ", viewRange=" + viewRange + ", xvfbDisplay=" + xvfbDisplay + ", xvfbWidth=" + xvfbWidth + ", xvfbHeight=" + xvfbHeight + ", igvMaxMemory=" + igvMaxMemory + '}';
     }
 
 }