From 3684934fd25c4941bd2d6ec8bc9dc7d760979f4e Mon Sep 17 00:00:00 2001
From: James Procter <j.procter@dundee.ac.uk>
Date: Fri, 10 Feb 2023 15:19:06 +0000
Subject: [PATCH] JAL-840 generate fragments of clustal.html documentation via
 ClustalxColurSchemeTest.testDocString()

---
 src/jalview/schemes/ClustalxColourScheme.java      |   61 ++++++++++++++++++++
 test/jalview/schemes/ClustalxColourSchemeTest.java |    8 +++
 2 files changed, 69 insertions(+)

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index 5a2d5dc..04097a8 100755
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -21,6 +21,7 @@
 package jalview.schemes;
 
 import java.awt.Color;
+import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
@@ -28,6 +29,7 @@ import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
+import jalview.util.ColorUtils;
 import jalview.util.Comparison;
 
 public class ClustalxColourScheme extends ResidueColourScheme
@@ -362,4 +364,63 @@ public class ClustalxColourScheme extends ResidueColourScheme
   {
     return false;
   }
+  public String toRuleRep()
+  {
+    makeColours();
+    HashMap<String, String> cols=new HashMap();
+    for (String res:ResidueProperties.aa) {
+      StringBuilder sb = new StringBuilder();
+      
+      int rnum=ResidueProperties.aaIndex[res.charAt(0)];
+      if (rnum<0 || rnum>=residueColour.length)
+      {
+        continue;
+      }
+      
+      ConsensusColour cc = residueColour[rnum];
+      if (cc==null)
+      {
+        continue;
+      }
+      //sb.append("Residue "+res+" ("+rnum+")");
+      //sb.append("\t");
+      sb.append(cc.c.toString());
+      double f=0;
+      sb.append("\t");
+      for (Consensus cons: cc.cons) {
+        if (cons.threshold==0 || f!=cons.threshold)
+        {
+          if (f!=0)
+          {
+
+              sb.append("}, {");
+          } else {
+          sb.append("{");
+          }
+        sb.append(cons.threshold);
+        sb.append(",");
+        f=cons.threshold;
+        } else {
+          sb.append(",");
+        }
+        sb.append(cons.maskstr);
+      }
+      sb.append("}");
+      String clxrep=sb.toString();
+      String xres = cols.get(clxrep);
+      if (xres==null) { xres = "";}
+      xres+=res;
+      cols.put(clxrep, xres);
+    }
+    StringBuilder sb = new StringBuilder();
+    for (String clxrep:cols.keySet())
+    {
+      sb.append(cols.get(clxrep));
+      sb.append("\t");
+      sb.append(clxrep);
+      sb.append("\n");
+      
+    }
+    return sb.toString();
+  }
 }
diff --git a/test/jalview/schemes/ClustalxColourSchemeTest.java b/test/jalview/schemes/ClustalxColourSchemeTest.java
index 6731465..d476d6e 100644
--- a/test/jalview/schemes/ClustalxColourSchemeTest.java
+++ b/test/jalview/schemes/ClustalxColourSchemeTest.java
@@ -151,4 +151,12 @@ public class ClustalxColourSchemeTest
     // viewport
     // assertEquals(cs.findColour('C', 0, al.getSequenceAt(0)), clustalPink);
   }
+  @Test
+  public void testDocString()
+  {
+    /* verify we have some sort of useful output */
+    ClustalxColourScheme x = new ClustalxColourScheme();
+    String out = x.toRuleRep();
+    System.out.print(out);
+  }
 }
-- 
1.7.10.2