X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FJalview2xmlTests.java;h=6dfa7291ae7756865c9d7c64d9b98ba960b625bf;hb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;hp=dc192344d467b59af43910b00c885d97ff59dad8;hpb=1889827c44c51f6353fe8619e5d44b421158af23;p=jalview.git

diff --git a/test/jalview/io/Jalview2xmlTests.java b/test/jalview/io/Jalview2xmlTests.java
index dc19234..6dfa729 100644
--- a/test/jalview/io/Jalview2xmlTests.java
+++ b/test/jalview/io/Jalview2xmlTests.java
@@ -44,7 +44,8 @@ public class Jalview2xmlTests
   @BeforeClass
   public static void setUpBeforeClass() throws Exception
   {
-    jalview.bin.Jalview.main(new String[] {"-props","test/src/jalview/io/testProps.jvprops"});
+    jalview.bin.Jalview.main(new String[]
+    { "-props", "test/src/jalview/io/testProps.jvprops" });
   }
 
   /**
@@ -54,12 +55,14 @@ public class Jalview2xmlTests
   public static void tearDownAfterClass() throws Exception
   {
     jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
-    
+
   }
+
   public int countDsAnn(jalview.viewmodel.AlignmentViewport avp)
   {
-    int numdsann=0;
-    for (SequenceI sq: avp.getAlignment().getDataset().getSequences()) {
+    int numdsann = 0;
+    for (SequenceI sq : avp.getAlignment().getDataset().getSequences())
+    {
       if (sq.getAnnotation() != null)
       {
         for (AlignmentAnnotation dssa : sq.getAnnotation())
@@ -73,35 +76,52 @@ public class Jalview2xmlTests
     }
     return numdsann;
   }
+
   @Test
   public void testRNAStructureRecovery() throws Exception
   {
     String inFile = "examples/RF00031_folded.stk";
-    String tfile = File.createTempFile("JalviewTest", ".jvp").getAbsolutePath();
-    AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(inFile, FormatAdapter.FILE);
-    assertTrue("Didn't read input file "+inFile, af!=null);
-    int olddsann=countDsAnn(af.getViewport());
-    assertTrue("Didn't find any dataset annotations",olddsann>0);
+    String tfile = File.createTempFile("JalviewTest", ".jvp")
+            .getAbsolutePath();
+    AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
+            inFile, FormatAdapter.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);
-    assertTrue("Failed to store as a project.",af.saveAlignment(tfile, "Jalview"));
+    assertTrue(
+            "Couldn't apply RNA helices colourscheme",
+            af.getViewport().getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
+    assertTrue("Failed to store as a project.",
+            af.saveAlignment(tfile, "Jalview"));
     af.closeMenuItem_actionPerformed(true);
-    af=null;
-    af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile, FormatAdapter.FILE);
-    assertTrue("Failed to import new project", af!=null);
-    int newdsann=countDsAnn(af.getViewport());
-    assertTrue("Differing numbers of dataset sequence annotation\nOriginally "+olddsann+" and now "+newdsann,olddsann==newdsann);
-    System.out.println("Read in same number of annotations as originally present ("+olddsann+")");
-    assertTrue("RNA helices colourscheme was not applied on import.",af.getViewport().getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
+    af = null;
+    af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
+            FormatAdapter.FILE);
+    assertTrue("Failed to import new project", af != null);
+    int newdsann = countDsAnn(af.getViewport());
+    assertTrue(
+            "Differing numbers of dataset sequence annotation\nOriginally "
+                    + olddsann + " and now " + newdsann,
+            olddsann == newdsann);
+    System.out
+            .println("Read in same number of annotations as originally present ("
+                    + olddsann + ")");
+    assertTrue(
+            "RNA helices colourscheme was not applied on import.",
+            af.getViewport().getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
   }
+
   @Test
   public void testTCoffeeScores() throws Exception
   {
-    String inFile = "examples/uniref50.fa",inAnnot="examples/uniref50.score_ascii";
-    String tfile = File.createTempFile("JalviewTest", ".jvp").getAbsolutePath();
-    AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(inFile, FormatAdapter.FILE);
-    assertTrue("Didn't read input file "+inFile, af!=null);
-    af.loadJalviewDataFile(inAnnot, FormatAdapter.FILE, null,null);
+    String inFile = "examples/uniref50.fa", inAnnot = "examples/uniref50.score_ascii";
+    String tfile = File.createTempFile("JalviewTest", ".jvp")
+            .getAbsolutePath();
+    AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
+            inFile, FormatAdapter.FILE);
+    assertTrue("Didn't read input file " + inFile, af != null);
+    af.loadJalviewDataFile(inAnnot, FormatAdapter.FILE, null, null);
     assertTrue(
             "Didn't set T-coffee colourscheme",
             af.getViewport().getGlobalColourScheme().getClass()
@@ -113,26 +133,40 @@ public class Jalview2xmlTests
                     jalview.schemes.ColourSchemeProperty.getColourName(af
                             .getViewport().getGlobalColourScheme())) != null);
 
-    assertTrue("Failed to store as a project.",af.saveAlignment(tfile, "Jalview"));
+    assertTrue("Failed to store as a project.",
+            af.saveAlignment(tfile, "Jalview"));
     af.closeMenuItem_actionPerformed(true);
-    af=null;
-    af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile, FormatAdapter.FILE);
-    assertTrue("Failed to import new project", af!=null);
-    assertTrue("Didn't set T-coffee colourscheme for imported project.",af.getViewport().getGlobalColourScheme().getClass().equals(jalview.schemes.TCoffeeColourScheme.class));
-    System.out.println("T-Coffee score shading successfully recovered from project.");
+    af = null;
+    af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
+            FormatAdapter.FILE);
+    assertTrue("Failed to import new project", af != null);
+    assertTrue(
+            "Didn't set T-coffee colourscheme for imported project.",
+            af.getViewport().getGlobalColourScheme().getClass()
+                    .equals(jalview.schemes.TCoffeeColourScheme.class));
+    System.out
+            .println("T-Coffee score shading successfully recovered from project.");
   }
+
   @Test
   public void testColourByAnnotScores() throws Exception
   {
-    String inFile = "examples/uniref50.fa",inAnnot="examples/testdata/uniref50_iupred.jva";
-    String tfile = File.createTempFile("JalviewTest", ".jvp").getAbsolutePath();
-    AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(inFile, FormatAdapter.FILE);
-    assertTrue("Didn't read input file "+inFile, af!=null);
-    af.loadJalviewDataFile(inAnnot, FormatAdapter.FILE, null,null);
-    AlignmentAnnotation[] aa = af.getViewport().getAlignment().getSequenceAt(0).getAnnotation("IUPredWS (Short)");
-    assertTrue("Didn't find any IUPred annotation to use to shade alignment.",aa!=null && aa.length>0);
-    AnnotationColourGradient cs = new jalview.schemes.AnnotationColourGradient(aa[0], null, AnnotationColourGradient.ABOVE_THRESHOLD);
-    AnnotationColourGradient gcs = new jalview.schemes.AnnotationColourGradient(aa[0], null, AnnotationColourGradient.BELOW_THRESHOLD);
+    String inFile = "examples/uniref50.fa", inAnnot = "examples/testdata/uniref50_iupred.jva";
+    String tfile = File.createTempFile("JalviewTest", ".jvp")
+            .getAbsolutePath();
+    AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
+            inFile, FormatAdapter.FILE);
+    assertTrue("Didn't read input file " + inFile, af != null);
+    af.loadJalviewDataFile(inAnnot, FormatAdapter.FILE, null, null);
+    AlignmentAnnotation[] aa = af.getViewport().getAlignment()
+            .getSequenceAt(0).getAnnotation("IUPredWS (Short)");
+    assertTrue(
+            "Didn't find any IUPred annotation to use to shade alignment.",
+            aa != null && aa.length > 0);
+    AnnotationColourGradient cs = new jalview.schemes.AnnotationColourGradient(
+            aa[0], null, AnnotationColourGradient.ABOVE_THRESHOLD);
+    AnnotationColourGradient gcs = new jalview.schemes.AnnotationColourGradient(
+            aa[0], null, AnnotationColourGradient.BELOW_THRESHOLD);
     cs.setSeqAssociated(true);
     gcs.setSeqAssociated(true);
     af.changeColour(cs);
@@ -144,56 +178,71 @@ public class Jalview2xmlTests
     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"));
+    assertTrue("Failed to store as a project.",
+            af.saveAlignment(tfile, "Jalview"));
     af.closeMenuItem_actionPerformed(true);
-    af=null;
-    af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile, FormatAdapter.FILE);
-    assertTrue("Failed to import new project", af!=null);
-    
+    af = null;
+    af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
+            FormatAdapter.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;
-    assertTrue("Didn't recover global colourscheme",_rcs!=null); 
-    assertTrue("Didn't recover annotation colour global scheme",_rcs instanceof AnnotationColourGradient);
+
+    ColourSchemeI _rcs = af.getViewport().getGlobalColourScheme();
+    ColourSchemeI _rgcs = af.getViewport().getAlignment().getGroups()
+            .get(0).cs;
+    assertTrue("Didn't recover global colourscheme", _rcs != null);
+    assertTrue("Didn't recover annotation colour global scheme",
+            _rcs instanceof AnnotationColourGradient);
     AnnotationColourGradient __rcs = (AnnotationColourGradient) _rcs;
-    assertTrue("Annotation colourscheme wasn't sequence associated",__rcs.isSeqAssociated());
+    assertTrue("Annotation colourscheme wasn't sequence associated",
+            __rcs.isSeqAssociated());
 
-    
-    boolean diffseqcols=false,diffgseqcols=false;
-    SequenceI[] sqs=af.getViewport().getAlignment().getSequencesArray();
-    for (int p=0,pSize=af.getViewport().getAlignment().getWidth();p<pSize && (!diffseqcols || !diffgseqcols);p++)
+    boolean diffseqcols = false, diffgseqcols = false;
+    SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray();
+    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]) != _rcs
+              .findColour(sqs[5].getCharAt(p), p, sqs[5]))
       {
         diffseqcols = true;
       }
     }
     assertTrue("Got Different sequence colours", diffseqcols);
-    System.out.println("Per sequence colourscheme (Background) successfully applied and recovered.");
-    
-    assertTrue("Didn't recover group colourscheme",_rgcs!=null); 
-    assertTrue("Didn't recover annotation colour group colourscheme",_rgcs instanceof AnnotationColourGradient);
+    System.out
+            .println("Per sequence colourscheme (Background) successfully applied and recovered.");
+
+    assertTrue("Didn't recover group colourscheme", _rgcs != null);
+    assertTrue("Didn't recover annotation colour group colourscheme",
+            _rgcs instanceof AnnotationColourGradient);
     __rcs = (AnnotationColourGradient) _rgcs;
-    assertTrue("Group Annotation colourscheme wasn't sequence associated",__rcs.isSeqAssociated());
-    
-    for (int p=0,pSize=af.getViewport().getAlignment().getWidth();p<pSize && (!diffseqcols || !diffgseqcols);p++)
+    assertTrue("Group Annotation colourscheme wasn't sequence associated",
+            __rcs.isSeqAssociated());
+
+    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]) != _rgcs
+              .findColour(sqs[2].getCharAt(p), p, sqs[2]))
       {
         diffgseqcols = true;
       }
     }
     assertTrue("Got Different group sequence colours", diffgseqcols);
-    System.out.println("Per sequence (Group) colourscheme successfully applied and recovered.");
+    System.out
+            .println("Per sequence (Group) colourscheme successfully applied and recovered.");
   }
+
   @Test
   public void gatherViewsHere() throws Exception
   {
     int origCount = Desktop.getAlignframes().length;
-    AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded("examples/exampleFile_2_7.jar", FormatAdapter.FILE);
-    assertTrue("Didn't read in the example file correctly.",af!=null);
-    assertTrue("Didn't gather the views in the example file.", Desktop.getAlignframes().length==1+origCount);
-    
+    AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
+            "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
+    assertTrue("Didn't read in the example file correctly.", af != null);
+    assertTrue("Didn't gather the views in the example file.",
+            Desktop.getAlignframes().length == 1 + origCount);
+
   }
 }