Chains#parse moved to repseq.io

milaboratory · Mar 28, 2017 · 86df8be · 86df8be
1 parent 185c727
commit 86df8be
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Showing 8 changed files with 9 additions and 29 deletions.
diff --git a/repseqio b/repseqio
diff --git a/src/main/java/com/milaboratory/mixcr/cli/ActionAlign.java b/src/main/java/com/milaboratory/mixcr/cli/ActionAlign.java
@@ -394,7 +394,7 @@ public boolean printWarnings() {
         }
 
         public Chains getChains() {
-            return Util.parseLoci(chains);
+            return Chains.parse(chains);
         }
 
         public boolean getWriteAllResults() {

diff --git a/src/main/java/com/milaboratory/mixcr/cli/ActionExportAlignmentsPretty.java b/src/main/java/com/milaboratory/mixcr/cli/ActionExportAlignmentsPretty.java
@@ -299,7 +299,7 @@ TLongHashSet getReadIds() {
         }
 
         public Chains getChain() {
-            return Util.parseLoci(chain);
+            return Chains.parse(chain);
         }
 
         @SuppressWarnings("unchecked")

diff --git a/src/main/java/com/milaboratory/mixcr/cli/ActionExportClonesPretty.java b/src/main/java/com/milaboratory/mixcr/cli/ActionExportClonesPretty.java
@@ -150,7 +150,7 @@ public static final class AParameters extends ActionParameters {
         public String csContain = null;
 
         public Chains getChain() {
-            return Util.parseLoci(chain);
+            return Chains.parse(chain);
         }
 
         public Filter<Clone> getFilter() {

diff --git a/src/main/java/com/milaboratory/mixcr/cli/ActionExportParameters.java b/src/main/java/com/milaboratory/mixcr/cli/ActionExportParameters.java
@@ -102,9 +102,9 @@ public Chains getChains() {
             if (!chains.equals("ALL"))
                 throw new ParameterException("Use -c without -l parameter.");
             System.out.println("WARNING: using of -l (--loci) option is deprecated; use -c (--chains) instead.");
-            return Util.parseLoci(chains_legacy);
+            return Chains.parse(chains_legacy);
         }
-        return Util.parseLoci(chains);
+        return Chains.parse(chains);
     }
 
     @SuppressWarnings("unchecked")

diff --git a/src/main/java/com/milaboratory/mixcr/cli/ActionExtendAlignments.java b/src/main/java/com/milaboratory/mixcr/cli/ActionExtendAlignments.java
@@ -106,7 +106,7 @@ private String getOutput() {
         }
 
         public Chains getChains() {
-            return Util.parseLoci(chains);
+            return Chains.parse(chains);
         }
 
         @Override

diff --git a/src/main/java/com/milaboratory/mixcr/cli/ActionFilterAlignments.java b/src/main/java/com/milaboratory/mixcr/cli/ActionFilterAlignments.java
@@ -158,7 +158,7 @@ protected List<String> getOutputFiles() {
         }
 
         public Chains getChains() {
-            return Util.parseLoci(chains);
+            return Chains.parse(chains);
         }
 
         public VDJCAlignmentsReader getInput() throws IOException {

diff --git a/src/main/java/com/milaboratory/mixcr/cli/Util.java b/src/main/java/com/milaboratory/mixcr/cli/Util.java
@@ -48,27 +48,7 @@ private Util() {
     }
 
     public static final DecimalFormat PERCENT_FORMAT = new DecimalFormat("#.##");
-
-    public static Chains parseLoci(String lociString) {
-        String[] split = lociString.split(",");
-        Chains chains = new Chains();
-        for (String s : split)
-            chains = chains.merge(parseLocus(s));
-        return chains;
-    }
-
-    private static Chains parseLocus(String value) {
-        switch (value.toLowerCase().trim()) {
-            case "tcr":
-                return Chains.TCR;
-            case "ig":
-                return Chains.IG;
-            case "all":
-                return Chains.ALL;
-        }
-        return new Chains(value);
-    }
-
+
     public static void writeReport(String input, String output,
                                    String commandLineArguments,
                                    String reportFileName,