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Merge branch 'features/JAL-2360colourSchemeApplicability' into features/JAL-2371colle...
[jalview.git] / test / jalview / io / Jalview2xmlTests.java
diff --git a/test/jalview/io/Jalview2xmlTests.java b/test/jalview/io/Jalview2xmlTests.java
index 3d53234..5b99fa1 100644 (file)
--- a/test/jalview/io/Jalview2xmlTests.java
+++ b/test/jalview/io/Jalview2xmlTests.java
@@ -41,9 +41,12 @@ import jalview.gui.AlignFrame;
 import jalview.gui.AlignmentPanel;
 import jalview.gui.Desktop;
 import jalview.gui.Jalview2XML;
+import jalview.gui.JvOptionPane;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.JalviewColourScheme;
+import jalview.schemes.RNAHelicesColour;
 import jalview.schemes.TCoffeeColourScheme;
 import jalview.structure.StructureImportSettings;
 import jalview.viewmodel.AlignmentViewport;
@@ -56,33 +59,42 @@ import java.util.Map;
 
 import org.testng.Assert;
 import org.testng.AssertJUnit;
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 @Test(singleThreaded = true)
 public class Jalview2xmlTests extends Jalview2xmlBase
 {
 
+  @Override
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   @Test(groups = { "Functional" })
   public void testRNAStructureRecovery() throws Exception
   {
     String inFile = "examples/RF00031_folded.stk";
     String tfile = File.createTempFile("JalviewTest", ".jvp")
             .getAbsolutePath();
-    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
-            FormatAdapter.FILE);
-    assertNotNull("Didn't read input file " + inFile, af);
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            inFile, DataSourceType.FILE);
+    assertTrue("Didn't read input file " + inFile, af != null);
     int olddsann = countDsAnn(af.getViewport());
     assertTrue("Didn't find any dataset annotations", olddsann > 0);
-    af.rnahelicesColour_actionPerformed(null);
-    assertTrue(
-            "Couldn't apply RNA helices colourscheme",
-            af.getViewport().getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
+    af.changeColour_actionPerformed(JalviewColourScheme.RNAHelices
+            .toString());
+    assertTrue("Couldn't apply RNA helices colourscheme", af.getViewport()
+            .getGlobalColourScheme() instanceof RNAHelicesColour);
     assertTrue("Failed to store as a project.",
-            af.saveAlignment(tfile, "Jalview"));
+            af.saveAlignment(tfile, FileFormat.Jalview));
     af.closeMenuItem_actionPerformed(true);
     af = null;
-    af = new FileLoader().LoadFileWaitTillLoaded(tfile, FormatAdapter.FILE);
-    assertNotNull("Failed to import new project", af);
+    af = new FileLoader().LoadFileWaitTillLoaded(tfile, DataSourceType.FILE);
+    assertTrue("Failed to import new project", af != null);
     int newdsann = countDsAnn(af.getViewport());
     assertTrue(
             "Differing numbers of dataset sequence annotation\nOriginally "
@@ -93,7 +105,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
                     + olddsann + ")");
     assertTrue(
             "RNA helices colourscheme was not applied on import.",
-            af.getViewport().getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
+            af.getViewport().getGlobalColourScheme() instanceof RNAHelicesColour);
   }
 
   @Test(groups = { "Functional" })
@@ -102,22 +114,23 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     String inFile = "examples/uniref50.fa", inAnnot = "examples/uniref50.score_ascii";
     String tfile = File.createTempFile("JalviewTest", ".jvp")
             .getAbsolutePath();
-    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
-            FormatAdapter.FILE);
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            inFile, DataSourceType.FILE);
     assertNotNull("Didn't read input file " + inFile, af);
-    af.loadJalviewDataFile(inAnnot, FormatAdapter.FILE, null, null);
+    af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null);
     assertSame("Didn't set T-coffee colourscheme", af.getViewport()
             .getGlobalColourScheme().getClass(), TCoffeeColourScheme.class);
     assertNotNull("Recognise T-Coffee score from string",
-            jalview.schemes.ColourSchemeProperty.getColour(af.getViewport()
-                    .getAlignment(), ColourSchemeProperty.getColourName(af
-                    .getViewport().getGlobalColourScheme())));
+            ColourSchemeProperty.getColourScheme(af.getViewport()
+                    .getAlignment(), af.getViewport()
+                    .getGlobalColourScheme().getSchemeName()));
 
     assertTrue("Failed to store as a project.",
-            af.saveAlignment(tfile, "Jalview"));
+            af.saveAlignment(tfile, FileFormat.Jalview));
     af.closeMenuItem_actionPerformed(true);
     af = null;
-    af = new FileLoader().LoadFileWaitTillLoaded(tfile, FormatAdapter.FILE);
+    af = new FileLoader().LoadFileWaitTillLoaded(tfile,
+            DataSourceType.FILE);
     assertNotNull("Failed to import new project", af);
     assertSame("Didn't set T-coffee colourscheme for imported project.", af
             .getViewport().getGlobalColourScheme().getClass(),
@@ -132,10 +145,9 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     String inFile = "examples/uniref50.fa", inAnnot = "examples/testdata/uniref50_iupred.jva";
     String tfile = File.createTempFile("JalviewTest", ".jvp")
             .getAbsolutePath();
-    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
-            FormatAdapter.FILE);
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile, DataSourceType.FILE);
     assertNotNull("Didn't read input file " + inFile, af);
-    af.loadJalviewDataFile(inAnnot, FormatAdapter.FILE, null, null);
+    af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null);
     AlignmentAnnotation[] aa = af.getViewport().getAlignment()
             .getSequenceAt(0).getAnnotation("IUPredWS (Short)");
     assertTrue(
@@ -151,23 +163,23 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     SequenceGroup sg = new SequenceGroup();
     sg.setStartRes(57);
     sg.setEndRes(92);
-    sg.cs = gcs;
+    sg.cs.setColourScheme(gcs);
     af.getViewport().getAlignment().addGroup(sg);
     sg.addSequence(af.getViewport().getAlignment().getSequenceAt(1), false);
     sg.addSequence(af.getViewport().getAlignment().getSequenceAt(2), true);
     af.alignPanel.alignmentChanged();
     assertTrue("Failed to store as a project.",
-            af.saveAlignment(tfile, "Jalview"));
+            af.saveAlignment(tfile, FileFormat.Jalview));
     af.closeMenuItem_actionPerformed(true);
     af = null;
-    af = new FileLoader().LoadFileWaitTillLoaded(tfile, FormatAdapter.FILE);
-    assertNotNull("Failed to import new project", af);
+    af = new FileLoader().LoadFileWaitTillLoaded(tfile, DataSourceType.FILE);
+    assertTrue("Failed to import new project", af != null);
 
     // check for group and alignment colourschemes
 
     ColourSchemeI _rcs = af.getViewport().getGlobalColourScheme();
     ColourSchemeI _rgcs = af.getViewport().getAlignment().getGroups()
-            .get(0).cs;
+            .get(0).getColourScheme();
     assertNotNull("Didn't recover global colourscheme", _rcs);
     assertTrue("Didn't recover annotation colour global scheme",
             _rcs instanceof AnnotationColourGradient);
@@ -180,8 +192,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     for (int p = 0, pSize = af.getViewport().getAlignment().getWidth(); p < pSize
             && (!diffseqcols || !diffgseqcols); p++)
     {
-      if (_rcs.findColour(sqs[0].getCharAt(p), p, sqs[0]) != _rcs
-              .findColour(sqs[5].getCharAt(p), p, sqs[5]))
+      if (_rcs.findColour(sqs[0].getCharAt(p), p, sqs[0], null, 0f) != _rcs
+              .findColour(sqs[5].getCharAt(p), p, sqs[5], null, 0f))
       {
         diffseqcols = true;
       }
@@ -200,8 +212,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     for (int p = 0, pSize = af.getViewport().getAlignment().getWidth(); p < pSize
             && (!diffseqcols || !diffgseqcols); p++)
     {
-      if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1]) != _rgcs
-              .findColour(sqs[2].getCharAt(p), p, sqs[2]))
+      if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1], null, 0f) != _rgcs
+              .findColour(sqs[2].getCharAt(p), p, sqs[2], null, 0f))
       {
         diffgseqcols = true;
       }
@@ -217,7 +229,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     int origCount = Desktop.getAlignFrames() == null ? 0 : Desktop
             .getAlignFrames().length;
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
-            "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
+            "examples/exampleFile_2_7.jar", DataSourceType.FILE);
     assertNotNull("Didn't read in the example file correctly.", af);
     assertTrue("Didn't gather the views in the example file.",
             Desktop.getAlignFrames().length == 1 + origCount);
@@ -230,7 +242,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     StructureImportSettings.setProcessSecondaryStructure(true);
     StructureImportSettings.setVisibleChainAnnotation(true);
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
-            "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
+            "examples/exampleFile_2_7.jar", DataSourceType.FILE);
     assertNotNull("Didn't read in the example file correctly.", af);
     AlignmentViewPanel sps = null;
     for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels())
@@ -291,7 +303,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   public void testCopyViewSettings() throws Exception
   {
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
-            "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
+            "examples/exampleFile_2_7.jar", DataSourceType.FILE);
     assertNotNull("Didn't read in the example file correctly.", af);
     AlignmentViewPanel sps = null, groups = null;
     for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels())
@@ -331,7 +343,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     Desktop.instance.closeAll_actionPerformed(null);
 
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
-            "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
+            "examples/exampleFile_2_7.jar", DataSourceType.FILE);
     Assert.assertEquals(Desktop.getAlignFrames().length, 1);
     String afid = af.getViewport().getSequenceSetId();
 
@@ -362,15 +374,15 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     {
       Assert.assertEquals(Desktop.getAlignFrames().length, 0);
     }
-    af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
-            FormatAdapter.FILE);
+    af = new FileLoader().LoadFileWaitTillLoaded(
+            tfile.getAbsolutePath(), DataSourceType.FILE);
     Assert.assertNotNull(af);
     Assert.assertEquals(
             Desktop.getAlignFrames().length,
             Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length);
     Assert.assertEquals(
-            oldviews,
-            Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length);
+            Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length,
+            oldviews);
   }
 
   /**
@@ -384,7 +396,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   {
     Desktop.instance.closeAll_actionPerformed(null);
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
-            "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
+            "examples/exampleFile_2_7.jar", DataSourceType.FILE);
     assertNotNull("Didn't read in the example file correctly.", af);
     String afid = af.getViewport().getSequenceSetId();
 
@@ -427,8 +439,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
       Assert.assertEquals(Desktop.getAlignFrames().length, 0);
     }
 
-    af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
-            FormatAdapter.FILE);
+    af = new FileLoader().LoadFileWaitTillLoaded(
+            tfile.getAbsolutePath(), DataSourceType.FILE);
     afid = af.getViewport().getSequenceSetId();
 
     for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
@@ -517,7 +529,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   {
     Desktop.instance.closeAll_actionPerformed(null);
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
-            "examples/uniref50.fa", FormatAdapter.FILE);
+            "examples/uniref50.fa", DataSourceType.FILE);
     assertNotNull("Didn't read in the example file correctly.", af);
     String afid = af.getViewport().getSequenceSetId();
     // make a second view of the alignment
@@ -595,9 +607,9 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     {
       Assert.assertEquals(Desktop.getAlignFrames().length, 0);
     }
-
-    af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
-            FormatAdapter.FILE);
+  
+    af = new FileLoader().LoadFileWaitTillLoaded(
+            tfile.getAbsolutePath(), DataSourceType.FILE);
     afid = af.getViewport().getSequenceSetId();
 
     for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid))
@@ -638,7 +650,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     Desktop.instance.closeAll_actionPerformed(null);
     String exampleFile = "examples/3W5V.pdb";
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(exampleFile,
-            FormatAdapter.FILE);
+            DataSourceType.FILE);
     assertNotNull("Didn't read in the example file correctly.", af);
     String afid = af.getViewport().getSequenceSetId();
 
@@ -687,7 +699,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     }
 
     AlignFrame restoredFrame = new FileLoader().LoadFileWaitTillLoaded(
-            tfile.getAbsolutePath(), FormatAdapter.FILE);
+            tfile.getAbsolutePath(), DataSourceType.FILE);
     String rfid = restoredFrame.getViewport().getSequenceSetId();
     AlignmentPanel[] rAlignPanels = Desktop.getAlignmentPanels(rfid);
     AlignmentViewPanel rap = rAlignPanels[0];