git://source.jalview.org / jalview.git / blobdiff
? search:
summary | shortlog | log | commit | commitdiff | tree
raw | inline | side by side
JAL-3304 option to export linked features in Jalview format
[jalview.git] / test / jalview / io / FeaturesFileTest.java
diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java
index 6f7bebe..090de6f 100644 (file)
--- a/test/jalview/io/FeaturesFileTest.java
+++ b/test/jalview/io/FeaturesFileTest.java
@@ -476,7 +476,7 @@ public class FeaturesFileTest
      */
     FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
     String exported = featuresFile
-            .printJalviewFormat(al.getSequencesArray(), fr, false);
+            .printJalviewFormat(al.getSequencesArray(), fr, false, false);
     String expected = "No Features Visible";
     assertEquals(expected, exported);
 
@@ -485,7 +485,7 @@ public class FeaturesFileTest
      */
     fr.setGroupVisibility("uniprot", true);
     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
-            true);
+            true, false);
     expected = "\nSTARTGROUP\tuniprot\n"
             + "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n"
             + "ENDGROUP\tuniprot\n\n"
@@ -499,7 +499,7 @@ public class FeaturesFileTest
     fr.setVisible("METAL");
     fr.setVisible("GAMMA-TURN");
     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
-            false);
+            false, false);
     expected = "METAL\tcc9900\n"
             + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
             + "\nSTARTGROUP\tuniprot\n"
@@ -513,7 +513,7 @@ public class FeaturesFileTest
      */
     fr.setVisible("Pfam");
     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
-            false);
+            false, false);
     /*
      * features are output within group, ordered by sequence and type
      */
@@ -539,14 +539,14 @@ public class FeaturesFileTest
             + "\ndesc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
             + "\ndesc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
-            false);
+            false, false);
     assertEquals(expected, exported);
 
     /*
      * include non-positional (overrides group not shown)
      */
     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
-            true);
+            true, false);
     expected = "METAL\tcc9900\n" + "Pfam\tff0000\n"
             + "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
             + "\nSTARTGROUP\tuniprot\n"
@@ -573,11 +573,11 @@ public class FeaturesFileTest
     FeatureRendererModel fr = (FeatureRendererModel) af.alignPanel
             .getFeatureRenderer();
     String exported = featuresFile.printGffFormat(al.getSequencesArray(),
-            fr, false);
+            fr, false, false);
     String gffHeader = "##gff-version 2\n";
     assertEquals(gffHeader, exported);
     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
-            true);
+            true, false);
     assertEquals(gffHeader, exported);
 
     /*
@@ -614,7 +614,7 @@ public class FeaturesFileTest
      * with no features displayed, exclude non-positional features
      */
     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
-            false);
+            false, false);
     assertEquals(gffHeader, exported);
 
     /*
@@ -623,7 +623,7 @@ public class FeaturesFileTest
     fr.setGroupVisibility("Uniprot", true);
     fr.setGroupVisibility("s3dm", false);
     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
-            true);
+            true, false);
     String expected = gffHeader
             + "FER_CAPAA\tUniprot\tDomain\t0\t0\t0.0\t.\t.\n";
     assertEquals(expected, exported);
@@ -635,7 +635,7 @@ public class FeaturesFileTest
     fr.setVisible("METAL");
     fr.setVisible("GAMMA-TURN");
     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
-            false);
+            false, false);
     // METAL feature has null group: description used for column 2
     expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n";
     assertEquals(expected, exported);
@@ -645,7 +645,7 @@ public class FeaturesFileTest
      */
     fr.setGroupVisibility("s3dm", true);
     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
-            false);
+            false, false);
     // METAL feature has null group: description used for column 2
     expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
             + "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n";
@@ -656,7 +656,7 @@ public class FeaturesFileTest
      */
     fr.setVisible("Pfam");
     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
-            false);
+            false, false);
     // Pfam feature columns include strand(+), phase(2), attributes
     expected = gffHeader
             + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
@@ -770,7 +770,7 @@ public class FeaturesFileTest
     fr.setVisible("METAL");
     fr.setColour("METAL", new FeatureColour(Color.PINK));
     String exported = featuresFile.printGffFormat(al.getSequencesArray(),
-            fr, false);
+            fr, false, false);
     String expected = gffHeader
             + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
             + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
@@ -785,7 +785,7 @@ public class FeaturesFileTest
     fc.setThreshold(1.1f);
     fr.setColour("METAL", fc);
     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
-            false);
+            false, false);
     expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n";
     assertEquals(expected, exported);
 
@@ -794,7 +794,7 @@ public class FeaturesFileTest
      */
     fc.setAboveThreshold(false);
     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
-            false);
+            false, false);
     expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
             + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
     assertEquals(expected, exported);
@@ -807,7 +807,7 @@ public class FeaturesFileTest
             "clin_sig"));
     fr.setFeatureFilter("METAL", filter);
     exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
-            false);
+            false, false);
     expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
     assertEquals(expected, exported);
   }
@@ -843,7 +843,7 @@ public class FeaturesFileTest
     fr.setColour("METAL", new FeatureColour(Color.PINK));
     String exported = featuresFile.printJalviewFormat(
             al.getSequencesArray(),
-            fr, false);
+            fr, false, false);
     String expected = "METAL\tffafaf\n\nSTARTGROUP\tgrp1\n"
             + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
             + "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n"
@@ -861,7 +861,7 @@ public class FeaturesFileTest
     fc.setThreshold(1.1f);
     fr.setColour("METAL", fc);
     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
-            false);
+            false, false);
     expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|above|1.1\n\n"
             + "STARTGROUP\tgrp1\n"
             + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
@@ -873,7 +873,7 @@ public class FeaturesFileTest
      */
     fc.setAboveThreshold(false);
     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
-            false);
+            false, false);
     expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|none\n\n"
             + "STARTGROUP\tgrp1\n"
             + "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
@@ -890,7 +890,7 @@ public class FeaturesFileTest
             "clin_sig"));
     fr.setFeatureFilter("METAL", filter);
     exported = featuresFile.printJalviewFormat(al.getSequencesArray(), fr,
-            false);
+            false, false);
     expected = "FER_CAPAA\tCath\tMETAL\t41\t41\t0.6\t.\t.\n";
     expected = "METAL\tscore|ffffff|000000|noValueMin|abso|0.0|2.0|none\n\n"
             + "STARTFILTERS\nMETAL\tclin_sig Contains benign\nENDFILTERS\n\n"