X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fproject%2FJalview2xmlTests.java;h=c070edb3fda271339dfd4e817bc01e04d8cac82d;hb=a327fd39320e482fad4b57f256f3e3c8ebcf015b;hp=783dd1cb90587a133b14488ea73bc03e3ea988dc;hpb=5d49f772d8dd53aba8907f37a244b00ed8f86a87;p=jalview.git

diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index 783dd1c..c070edb 100644
--- a/test/jalview/project/Jalview2xmlTests.java
+++ b/test/jalview/project/Jalview2xmlTests.java
@@ -53,6 +53,7 @@ import jalview.api.ViewStyleI;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.GeneLocus;
 import jalview.datamodel.HiddenSequences;
@@ -238,8 +239,9 @@ public class Jalview2xmlTests extends Jalview2xmlBase
 
     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++)
+    for (int p = 0,
+            pSize = af.getViewport().getAlignment().getWidth(); p < pSize
+                    && (!diffseqcols || !diffgseqcols); p++)
     {
       if (_rcs.findColour(sqs[0].getCharAt(p), p, sqs[0], null, 0f) != _rcs
               .findColour(sqs[5].getCharAt(p), p, sqs[5], null, 0f))
@@ -258,8 +260,9 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     assertTrue(__rcs.isSeqAssociated(),
             "Group Annotation colourscheme wasn't sequence associated");
 
-    for (int p = 0, pSize = af.getViewport().getAlignment()
-            .getWidth(); p < pSize && (!diffseqcols || !diffgseqcols); p++)
+    for (int p = 0,
+            pSize = af.getViewport().getAlignment().getWidth(); p < pSize
+                    && (!diffseqcols || !diffgseqcols); p++)
     {
       if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1], null,
               0f) != _rgcs.findColour(sqs[2].getCharAt(p), p, sqs[2], null,
@@ -590,6 +593,14 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3"));
     assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.2b1"));
     assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.0b2", "2.8.0b1"));
+    /*
+     * test for patch release versions
+     */
+    assertFalse(Jalview2XML.isVersionStringLaterThan("2.11.3.0", "2.11.2"));
+    assertTrue(Jalview2XML.isVersionStringLaterThan("2.11.3.0","2.11.4"));
+    assertFalse(Jalview2XML.isVersionStringLaterThan("2.12.2.0b1","2.12.2.0"));
+    assertFalse(Jalview2XML.isVersionStringLaterThan("2.12.2.3","2.12.2.2"));
+
   }
 
   /**
@@ -808,8 +819,94 @@ public class Jalview2xmlTests extends Jalview2xmlBase
               "Mismatch PDBEntry 'Type'");
       Assert.assertNotNull(recov.getFile(),
               "Recovered PDBEntry should have a non-null file entry");
-      Assert.assertEquals(recov.getFile().toLowerCase(Locale.ENGLISH).lastIndexOf("pdb"),recov.getFile().length()-3, "Recovered PDBEntry file should have PDB suffix");
+      Assert.assertEquals(
+              recov.getFile().toLowerCase(Locale.ENGLISH)
+                      .lastIndexOf("pdb"),
+              recov.getFile().length() - 3,
+              "Recovered PDBEntry file should have PDB suffix");
+    }
+  }
+
+  /**
+   * Configure an alignment and a sub-group each with distinct colour schemes,
+   * Conservation and PID thresholds, and confirm these are restored from the
+   * saved project.
+   * 
+   * @throws IOException
+   */
+  @Test(groups = { "Functional" })
+  public void testStoreAndRecoverAnnotationRowElementColours()
+          throws IOException
+  {
+    Desktop.instance.closeAll_actionPerformed(null);
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded("SEQ\tMNQ",
+            DataSourceType.PASTE);
+
+    AlignViewport av = af.getViewport();
+    AlignmentI al = av.getAlignment();
+    SequenceI fsq;
+    fsq = al.getSequenceAt(0);
+    Annotation annots[] = new Annotation[fsq.getLength()];
+    AlignmentAnnotation ala = new AlignmentAnnotation("Colour", "Annots",
+            annots);
+    annots[0] = new Annotation(1.0f);
+    annots[1] = new Annotation(2.0f);
+    annots[2] = new Annotation(3.0f);
+    annots[0].colour = Color.RED;
+    annots[1].colour = Color.GREEN;
+    annots[2].colour = Color.BLUE;
+    ala.validateRangeAndDisplay();
+    al.getSequenceAt(0).addAlignmentAnnotation(ala);
+    al.addAnnotation(ala);
+    /*
+     * and colour by annotation
+     */
+    AnnotationColourGradient acg = new AnnotationColourGradient(ala,
+            af.alignPanel.av.getGlobalColourScheme(), 0);
+    acg.setSeqAssociated(true);
+    acg.setPredefinedColours(true);
+    af.changeColour(acg);
+    Color seqcol[] = new Color[3];
+    for (int iStart=fsq.findIndex(fsq.getStart()),i=0;i<3;i++) {
+      seqcol[i] = af.alignPanel.getSeqPanel().seqCanvas.getSequenceRenderer().getResidueColour(fsq, iStart+i, null);
+    }
+    /*
+     * save project, close windows, reload project, verify
+     */
+    File tfile = File.createTempFile(
+            "testStoreAndRecoverAnnotRowElemColors", ".jvp");
+    tfile.deleteOnExit();
+    new Jalview2XML(false).saveState(tfile);
+    //Desktop.instance.closeAll_actionPerformed(null);
+    af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
+            DataSourceType.FILE);
+    Assert.assertNotNull(af, "Failed to reload project");
+    /*
+     * verify alignment annotation has colors
+     */
+    av = af.getViewport();
+    
+    ColourSchemeI loadedCscheme = av.getGlobalColourScheme();
+    Assert.assertTrue(loadedCscheme instanceof AnnotationColourGradient,"Didn't apply Annotation colour gradient");
+    acg = (AnnotationColourGradient) loadedCscheme;
+    assertTrue(acg.isSeqAssociated());
+    assertTrue(acg.isPredefinedColours());
+
+    al = av.getAlignment();
+    fsq = al.getSequenceAt(0);
+    ala = fsq.getAnnotation()[0];
+    Assert.assertNotNull(ala, "No annotation row recovered");
+    Assert.assertNotNull(ala.annotations);
+    for (int iStart = al.getSequenceAt(0)
+            .findIndex(al.getSequenceAt(0).getStart()), i = 0; i < 3; i++)
+    {
+      Assert.assertTrue(ala.annotations[i].colour!=null);
+      Assert.assertTrue(ala.annotations[i].colour.equals(annots[i].colour));
+      Color newseqcol = af.alignPanel.getSeqPanel().seqCanvas.getSequenceRenderer().getResidueColour(fsq, iStart+i, null);
+      Assert.assertTrue(seqcol[i].equals(newseqcol),"Sequence shading is different");
+
     }
+    
   }
 
   /**
@@ -1388,4 +1485,45 @@ public class Jalview2xmlTests extends Jalview2xmlBase
 
     assertNull(af.alignPanel.getOverviewPanel());
   }
+
+  /**
+   * Test that a view from an older version of Jalview is restored with Overview automatically shown when the preference is set
+   * 
+   * @throws Exception
+   */
+  @Test(groups = { "Functional" }, enabled = true)
+  public void testAutoShowOverviewForLegacyProjects() throws Exception
+  {
+    Desktop.instance.closeAll_actionPerformed(null);
+    Cache.setProperty("SHOW_OVERVIEW", "true");
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            "examples/exampleFile.jvp", DataSourceType.FILE);
+
+    Cache.setProperty("SHOW_OVERVIEW", "false");
+    assertNotNull(af.alignPanel.getOverviewPanel());
+  }
+
+  /**
+   * Test that loading example.jvp, doing some stuff, then hitting reload
+   * doesn't leave the modified window still open
+   * 
+   * See JAL-4127 - interactively performing the same actions and reloading
+   * works fine, but programmatically they do not
+   * 
+   * @throws Exception
+   */
+  @Test(groups = {"Functional"}, enabled=false)
+  public void testReloadActuallyReloads() throws Exception
+  {
+    Desktop.instance.closeAll_actionPerformed(null);
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            "examples/exampleFile.jvp", DataSourceType.FILE);
+    af.getViewport().getColumnSelection().addElement(3);
+    af.hideSelColumns_actionPerformed(null);
+    af.newView("new", true);
+    af.reload_actionPerformed(null);
+    Thread.sleep(30);
+    // af exists still but isn't shown
+    assertTrue(af.isClosed());
+  }
 }