X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FJalview2xmlTests.java;h=dc192344d467b59af43910b00c885d97ff59dad8;hb=47168f025aefdaa044802bd5f8f510ffe43a4808;hp=2e19e99025bb37012e1c9e25e9c00a58f3d8c7fb;hpb=9e7813462e67e9ef34f55aa419c0e7687277a271;p=jalview.git

diff --git a/test/jalview/io/Jalview2xmlTests.java b/test/jalview/io/Jalview2xmlTests.java
index 2e19e99..dc19234 100644
--- a/test/jalview/io/Jalview2xmlTests.java
+++ b/test/jalview/io/Jalview2xmlTests.java
@@ -1,9 +1,33 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.io;
 
 import static org.junit.Assert.*;
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.ColourSchemeI;
 
 import java.io.File;
 
@@ -29,7 +53,8 @@ public class Jalview2xmlTests
   @AfterClass
   public static void tearDownAfterClass() throws Exception
   {
-    jalview.gui.Desktop.instance.quit();
+    jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
+    
   }
   public int countDsAnn(jalview.viewmodel.AlignmentViewport avp)
   {
@@ -57,6 +82,8 @@ public class Jalview2xmlTests
     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"));
     af.closeMenuItem_actionPerformed(true);
     af=null;
@@ -65,6 +92,108 @@ public class Jalview2xmlTests
     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);
+    assertTrue(
+            "Didn't set T-coffee colourscheme",
+            af.getViewport().getGlobalColourScheme().getClass()
+                    .equals(jalview.schemes.TCoffeeColourScheme.class));
+    assertTrue(
+            "Recognise T-Coffee score from string",
+            jalview.schemes.ColourSchemeProperty.getColour(af.getViewport()
+                    .getAlignment(),
+                    jalview.schemes.ColourSchemeProperty.getColourName(af
+                            .getViewport().getGlobalColourScheme())) != null);
+
+    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.");
+  }
+  @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);
+    cs.setSeqAssociated(true);
+    gcs.setSeqAssociated(true);
+    af.changeColour(cs);
+    SequenceGroup sg = new SequenceGroup();
+    sg.setStartRes(57);
+    sg.setEndRes(92);
+    sg.cs = 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.closeMenuItem_actionPerformed(true);
+    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);
+    AnnotationColourGradient __rcs = (AnnotationColourGradient) _rcs;
+    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++)
+    {
+      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);
+    __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++)
+    {
+    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.");
+  }
+  @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);
+    
+  }
 }