X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fclade_analysis%2FCladeAnalysisTest.java;h=3d1f4b98246d6ccf3b01acd3a15ace2d4c69178a;hb=a0d44ec0ea329861626d05136c2ac28ae3ee4ed9;hp=7c1d38bc0d52e4f2ad6d2ac05ce96bea5eadf5b4;hpb=3830877262aa9098f0bdecc7e7d3b171f6d8f527;p=jalview.git diff --git a/forester/java/src/org/forester/clade_analysis/CladeAnalysisTest.java b/forester/java/src/org/forester/clade_analysis/CladeAnalysisTest.java index 7c1d38b..3d1f4b9 100644 --- a/forester/java/src/org/forester/clade_analysis/CladeAnalysisTest.java +++ b/forester/java/src/org/forester/clade_analysis/CladeAnalysisTest.java @@ -590,99 +590,120 @@ public class CladeAnalysisTest { } return true; } - + private static boolean testCladeAnalysis3() { try { - /* - final Result2 res1 = new Result2(); - res1.addGreatestCommonPrefix( "A.1.1", 0.3 ); - res1.addGreatestCommonPrefix( "A.1.2", 0.3 ); - res1.addGreatestCommonPrefix( "A.1.3", 0.3 ); - res1.addGreatestCommonPrefix( "B.1", 0.1 ); - - List x = ForesterUtil.spliIntoPrefixes( "A.1.2.3.4", "." ); - // System.out.println( x ); - x =ForesterUtil.spliIntoPrefixes( "A", "." ); - // System.out.println( x ); - - - res1.analyzeGreatestCommonPrefixes( ); - - final Result2 res2 = new Result2("."); - res2.addGreatestCommonPrefix( "A.1.1.1", 0.1 ); - res2.addGreatestCommonPrefix( "A.1", 0.7 ); - res2.addGreatestCommonPrefix( "A.1.2", 0.1 ); - res2.addGreatestCommonPrefix( "B.1", 0.1 ); - res2.analyzeGreatestCommonPrefixes( ); - */ - final Result2 res3 = new Result2("."); - res3.addGreatestCommonPrefix( "A.1.1.1", 0.1 ); - res3.addGreatestCommonPrefix( "A.1.1.1.1", 0.6 ); - res3.addGreatestCommonPrefix( "A.1", 0.1 ); - res3.addGreatestCommonPrefix( "A.1.2", 0.1 ); - res3.addGreatestCommonPrefix( "B.1", 0.1 ); - res3.analyzeGreatestCommonPrefixes( ); - - final Result2 res33 = new Result2("."); - res33.addGreatestCommonPrefix( "A.1.1.1", 0.1 ); - res33.addGreatestCommonPrefix( "A.1.1.1.1", 0.3 ); - res33.addGreatestCommonPrefix( "A.1", 0.1 ); - res33.addGreatestCommonPrefix( "A.1.2", 0.1 ); - res33.addGreatestCommonPrefix( "B.1", 0.1 ); - res33.addGreatestCommonPrefix( "B.1.1.1", 0.3 ); - res33.analyzeGreatestCommonPrefixes( ); - - /* - final Result2 res4 = new Result2(); - res4.addGreatestCommonPrefix( "A.1.1.1.1", 0.35); - res4.addGreatestCommonPrefix( "A.1.1.1.2", 0.35 ); - res4.addGreatestCommonPrefix( "A.1", 0.1 ); - res4.addGreatestCommonPrefix( "A.1.2", 0.1 ); - res4.addGreatestCommonPrefix( "B.1", 0.1 ); - res4.analyzeGreatestCommonPrefixes( ); - - final Result2 res5 = new Result2(); - res5.addGreatestCommonPrefix( "A.1.1.1.1", 0.2); - res5.addGreatestCommonPrefix( "C.2.3", 0.2 ); - res5.addGreatestCommonPrefix( "A.1.5", 0.1 ); - res5.addGreatestCommonPrefix( "A.3.1.4", 0.2 ); - res5.addGreatestCommonPrefix( "B.1.1", 0.2 ); - res5.addGreatestCommonPrefix( "B.1.2", 0.09 ); - res5.addGreatestCommonPrefix( "D.1.1.1.1", 0.01 ); - res5.analyzeGreatestCommonPrefixes( ); - - final Result2 res6 = new Result2(); - res6.addGreatestCommonPrefix( "A.1.1.1", 0.05 ); - res6.addGreatestCommonPrefix( "A.1.1.1.1", 0.65 ); - res6.addGreatestCommonPrefix( "A.1", 0.1 ); - res6.addGreatestCommonPrefix( "A.1.2", 0.1 ); - res6.addGreatestCommonPrefix( "B.1", 0.1 ); - res6.analyzeGreatestCommonPrefixes( ); - - final Result2 res7 = new Result2(); - res7.addGreatestCommonPrefix( "A.1.1.1", 0.07 ); - res7.addGreatestCommonPrefix( "A.1.1.1.1", 0.9 ); - res7.addGreatestCommonPrefix( "A.1", 0.01 ); - res7.addGreatestCommonPrefix( "A.1.2", 0.01 ); - res7.addGreatestCommonPrefix( "B.1", 0.01 ); - res7.analyzeGreatestCommonPrefixes( ); - - final Result2 res8 = new Result2("_/_"); - res8.addGreatestCommonPrefix( "AA_/_abc_/_def", 0.07 ); - res8.addGreatestCommonPrefix( "AA_/_abc_/_sfc", 0.9 ); - res8.addGreatestCommonPrefix( "AA_/_abc_/_xcd", 0.01 ); - res8.addGreatestCommonPrefix( "AA_/_abc_/_memr", 0.01 ); - res8.addGreatestCommonPrefix( "AA_/_abc_/_fkem_/_odem", 0.01 ); - res8.analyzeGreatestCommonPrefixes( ); - - final Result2 res9 = new Result2("_/_"); - res9.addGreatestCommonPrefix( "AA_/_abc_/_def", 0.07 ); - res9.addGreatestCommonPrefix( "AA_/_abc_/_sfc", 0.6 ); - res9.addGreatestCommonPrefix( "AA_/_abc_/_xcd", 0.01 ); - res9.addGreatestCommonPrefix( "AA_/_abc_/_memr", 0.01 ); - res9.addGreatestCommonPrefix( "AA_/_abc_/_fkem_/_odem", 0.01 ); - res9.addGreatestCommonPrefix( "BB_/_fke_/_dme_/_nx2", 0.3 ); - res9.analyzeGreatestCommonPrefixes( );*/ + final Result2 res1 = new Result2(); + res1.addGreatestCommonPrefix( "A.1.1", 0.3 ); + res1.addGreatestCommonPrefix( "A.1.2", 0.3 ); + res1.addGreatestCommonPrefix( "A.1.3", 0.3 ); + res1.addGreatestCommonPrefix( "B.1", 0.1 ); + res1.analyzeGreatestCommonPrefixes( 0.3 ); + System.out.print( res1.toString()); + System.out.println( "------------------------- "); + System.out.println(); + + final Result2 res2 = new Result2( "." ); + res2.addGreatestCommonPrefix( "A.1.1.1", 0.1 ); + res2.addGreatestCommonPrefix( "A.1", 0.7 ); + res2.addGreatestCommonPrefix( "A.1.2", 0.1 ); + res2.addGreatestCommonPrefix( "B.1", 0.1 ); + res2.analyzeGreatestCommonPrefixes( 0.3 ); + System.out.print( res2.toString()); + System.out.println( "------------------------- "); + System.out.println(); + + final Result2 res3 = new Result2( "." ); + res3.addGreatestCommonPrefix( "A.1.1.1", 0.1 ); + res3.addGreatestCommonPrefix( "A.1.1.1.1", 0.6 ); + res3.addGreatestCommonPrefix( "A.1", 0.1 ); + res3.addGreatestCommonPrefix( "A.1.2", 0.1 ); + res3.addGreatestCommonPrefix( "B.1", 0.1 ); + res3.analyzeGreatestCommonPrefixes( 0.3 ); + System.out.print( res3.toString()); + System.out.println( "------------------------- "); + System.out.println(); + + final Result2 res33 = new Result2( "." ); + res33.addGreatestCommonPrefix( "A.1.1.1", 0.1 ); + res33.addGreatestCommonPrefix( "A.1.1.1.1", 0.3 ); + res33.addGreatestCommonPrefix( "A.1", 0.1 ); + res33.addGreatestCommonPrefix( "A.1.2", 0.1 ); + res33.addGreatestCommonPrefix( "B.1", 0.1 ); + res33.addGreatestCommonPrefix( "B.1.1.1", 0.3 ); + res33.analyzeGreatestCommonPrefixes( 0.3 ); + System.out.print( res33.toString()); + System.out.println( "------------------------- "); + System.out.println(); + + final Result2 res4 = new Result2(); + res4.addGreatestCommonPrefix( "A.1.1.1.1", 0.35 ); + res4.addGreatestCommonPrefix( "A.1.1.1.2", 0.35 ); + res4.addGreatestCommonPrefix( "A.1", 0.1 ); + res4.addGreatestCommonPrefix( "A.1.2", 0.1 ); + res4.addGreatestCommonPrefix( "B.1", 0.1 ); + res4.analyzeGreatestCommonPrefixes( 0.3 ); + System.out.print( res4.toString()); + System.out.println( "------------------------- "); + System.out.println(); + + final Result2 res5 = new Result2(); + res5.addGreatestCommonPrefix( "A.1.1.1.1", 0.2 ); + res5.addGreatestCommonPrefix( "C.2.3", 0.2 ); + res5.addGreatestCommonPrefix( "A.1.5", 0.1 ); + res5.addGreatestCommonPrefix( "A.3.1.4", 0.2 ); + res5.addGreatestCommonPrefix( "B.1.1", 0.2 ); + res5.addGreatestCommonPrefix( "B.1.2", 0.09 ); + res5.addGreatestCommonPrefix( "D.1.1.1.1", 0.01 ); + res5.analyzeGreatestCommonPrefixes( 0.3 ); + System.out.print( res5.toString()); + System.out.println( "------------------------- "); + System.out.println(); + + final Result2 res6 = new Result2(); + res6.addGreatestCommonPrefix( "A.1.1.1", 0.05 ); + res6.addGreatestCommonPrefix( "A.1.1.1.1", 0.65 ); + res6.addGreatestCommonPrefix( "A.1", 0.1 ); + res6.addGreatestCommonPrefix( "A.1.2", 0.1 ); + res6.addGreatestCommonPrefix( "B.1", 0.1 ); + res6.analyzeGreatestCommonPrefixes( 0.3 ); + System.out.print( res6.toString()); + System.out.println( "------------------------- "); + System.out.println(); + + final Result2 res7 = new Result2(); + res7.addGreatestCommonPrefix( "A.1.1.1", 0.07 ); + res7.addGreatestCommonPrefix( "A.1.1.1.1", 0.9 ); + res7.addGreatestCommonPrefix( "A.1", 0.01 ); + res7.addGreatestCommonPrefix( "A.1.2", 0.01 ); + res7.addGreatestCommonPrefix( "B.1", 0.01 ); + res7.analyzeGreatestCommonPrefixes( 0.3 ); + System.out.print( res7.toString()); + System.out.println( "------------------------- "); + System.out.println(); + + final Result2 res8 = new Result2( "_/_" ); + res8.addGreatestCommonPrefix( "AA_/_abc_/_def", 0.07 ); + res8.addGreatestCommonPrefix( "AA_/_abc_/_sfc", 0.9 ); + res8.addGreatestCommonPrefix( "AA_/_abc_/_xcd", 0.01 ); + res8.addGreatestCommonPrefix( "AA_/_abc_/_memr", 0.01 ); + res8.addGreatestCommonPrefix( "AA_/_abc_/_fkem_/_odem", 0.01 ); + res8.analyzeGreatestCommonPrefixes( 0.3 ); + System.out.print( res8.toString()); + System.out.println( "------------------------- "); + System.out.println(); + + final Result2 res9 = new Result2( "_/_" ); + res9.addGreatestCommonPrefix( "AA_/_abc_/_def", 0.07 ); + res9.addGreatestCommonPrefix( "AA_/_abc_/_sfc", 0.6 ); + res9.addGreatestCommonPrefix( "AA_/_abc_/_xcd", 0.01 ); + res9.addGreatestCommonPrefix( "AA_/_abc_/_memr", 0.01 ); + res9.addGreatestCommonPrefix( "AA_/_abc_/_fkem_/_odem", 0.01 ); + res9.addGreatestCommonPrefix( "BB_/_fke_/_dme_/_nx2", 0.3 ); + res9.analyzeGreatestCommonPrefixes( 0.3 ); + System.out.print( res9.toString()); + System.out.println( "------------------------- "); + System.out.println(); } catch ( final Exception e ) { e.printStackTrace( System.out );