X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fproject%2FJalview2xmlTests.java;h=dcf8febdc81d9cfddd220e86967300e24361f5f0;hb=96f727b57ac588f9307116b79a7f1ab67dbff39b;hp=9c1b32ffe4727fe2f03b09aea9a6d1a047c76632;hpb=b122ba188c2ffcbb302809bafc02058e355643ee;p=jalview.git

diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index 9c1b32f..dcf8feb 100644
--- a/test/jalview/project/Jalview2xmlTests.java
+++ b/test/jalview/project/Jalview2xmlTests.java
@@ -102,6 +102,7 @@ import jalview.schemes.StrandColourScheme;
 import jalview.schemes.TCoffeeColourScheme;
 import jalview.structure.StructureImportSettings;
 import jalview.util.MapList;
+import jalview.util.Platform;
 import jalview.util.matcher.Condition;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
@@ -1550,12 +1551,12 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   @Test(groups = { "Functional" })
   public void testMatrixToFloatsAndBack()
   {
-    int imax=2000;
-    int i=imax;
-    SequenceI sq = new Sequence("dummy","SEQ");
-    while (sq.getLength()<i)
+    int imax = 2000;
+    int i = imax;
+    SequenceI sq = new Sequence("dummy", "SEQ");
+    while (sq.getLength() < i)
     {
-      sq.setSequence(sq.getSequenceAsString()+'Q');
+      sq.setSequence(sq.getSequenceAsString() + 'Q');
     }
     float[][] paevals = new float[i][i];
     for (i = imax - 1; i >= 0; i--)
@@ -1575,16 +1576,17 @@ public class Jalview2xmlTests extends Jalview2xmlBase
             sq.getLength(), sq.getLength());
     assertEquals(vals[3][4], paevals[3][4]);
     assertEquals(vals[4][3], paevals[4][3]);
-    
+
     // test recovery
-    for (i=0;i<imax;i++)
+    for (i = 0; i < imax; i++)
     {
-      for (int j=0;j<imax;j++)
+      for (int j = 0; j < imax; j++)
       {
-        assertEquals(vals[i][j],paevals[i][j]);
+        assertEquals(vals[i][j], paevals[i][j]);
       }
     }
   }
+
   @Test(groups = { "Functional" })
   public void testPAEsaveRestore() throws Exception
   {
@@ -1614,7 +1616,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
             sq.getLength(), sq.getLength());
     assertEquals(vals[3][4], paevals[3][4]);
     assertEquals(vals[4][3], paevals[4][3]);
-    dummyMat.setGroupSet(GroupSet.makeGroups(dummyMat, false,0.5f, false));
+    dummyMat.setGroupSet(GroupSet.makeGroups(dummyMat, false, 0.5f, false));
     Assert.assertNotSame(dummyMat.getNewick(), "");
     AlignmentAnnotation paeCm = sq.addContactList(dummyMat);
     al.addAnnotation(paeCm);
@@ -1688,12 +1690,13 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     Assert.assertEquals(restoredMat.getNewick(), dummyMat.getNewick());
 
     // verify no duplicate PAE matrix data when new view created and saved
-    
+
     // add reference annotations to view first, then copy
-    AlignmentUtils.addReferenceAnnotationTo(newAl, newAl.getSequenceAt(0), newSeq.getAnnotation()[0],null);
-    
+    AlignmentUtils.addReferenceAnnotationTo(newAl, newAl.getSequenceAt(0),
+            newSeq.getAnnotation()[0], null);
+
     AlignmentViewPanel newview = af.newView("copy of PAE", true);
-    
+
     // redundant asserts here check all is good with the new view firest...
     AlignmentI newviewAl = newview.getAlignment();
     SequenceI newviewSeq = newviewAl.getSequenceAt(0);
@@ -1702,16 +1705,17 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     Assert.assertEquals(newviewSeq.getAnnotation()[0].graph, paeCm.graph);
     // check we have just one contact matrix mapping
     Assert.assertEquals(newviewSeq.getContactMaps().size(), 1);
-    
+
     // and can be found for the annotation on the sequence
     ContactMatrixI newviewMat = newviewSeq
             .getContactMatrixFor(newviewSeq.getAnnotation()[0]);
     Assert.assertNotNull(newviewMat);
 
     Assert.assertTrue(newviewMat == restoredMat);
-    
-    // save the two views and restore. Now look at visible annotation to check all views have shared refs.
-    
+
+    // save the two views and restore. Now look at visible annotation to check
+    // all views have shared refs.
+
     tfile = File.createTempFile("testStoreAndRecoverPAEmatrixTwoViews",
             ".jvp");
     new Jalview2XML(false).saveState(tfile);
@@ -1723,19 +1727,93 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     AlignmentAnnotation view1aa = newAl.getSequenceAt(0).getAnnotation()[0];
 
     newviewAl = af.getAlignPanels().get(1).getAlignment();
-    AlignmentAnnotation view2aa = newviewAl.getSequenceAt(0).getAnnotation()[0];
+    AlignmentAnnotation view2aa = newviewAl.getSequenceAt(0)
+            .getAnnotation()[0];
 
-    // annotations are shared across alignment views - so should still have an identical pair of annotations.
-    Assert.assertTrue(view1aa==view2aa);
+    // annotations are shared across alignment views - so should still have an
+    // identical pair of annotations.
+    Assert.assertTrue(view1aa == view2aa);
     // identical annotations means identical contact matrix mappings
-    Assert.assertEquals(newAl.getDataset().getSequenceAt(0).getContactMaps().size(), 1);
+    Assert.assertEquals(
+            newAl.getDataset().getSequenceAt(0).getContactMaps().size(), 1);
 
-    // TODO Verify when distinct mappable PAEs are created, only one PAE dataset is actually held.
+    // TODO Verify when distinct mappable PAEs are created, only one PAE dataset
+    // is actually held.
     // Assert.assertTrue(view1aa!=view2aa);
     // restoredMat = newAl.getContactMatrixFor(view1aa);
     // newviewMat = newviewAl.getContactMatrixFor(view2aa);
     // Assert.assertTrue(restoredMat!=newviewMat);
-    
+
+  }
+
+  @Test(groups = "Functional")
+  public void testStoreAndRestoreIDwidthAndAnnotationHeight()
+          throws IOException
+  {
+    Desktop.instance.closeAll_actionPerformed(null);
+    final String SECONDVIEW = "With Diffferent IDwidth";
+    // create a new tempfile
+    File tempfile = File.createTempFile("jvIdWidthStoreRestore", "jvp");
+
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            "examples/exampleFile.jvp", DataSourceType.FILE);
+    assertNotNull(af, "Didn't read in the example file correctly.");
+    // FIXME JAL-4281 test made platform dependent to pass, but probably
+    // shouldn't be platform dependent
+    assertEquals(af.alignPanel.getAlignViewport().getIdWidth(),
+            Platform.isAMacAndNotJS() ? 144 : 138,
+            "Legacy project import should have fixed ID width");
+    assertTrue(
+            af.alignPanel.getIdPanel().getIdCanvas().isManuallyAdjusted());
+
+    af.alignPanel.getAlignViewport().setIdWidth(100);
+    af.alignPanel.updateLayout();
+    assertTrue(
+            af.alignPanel.getIdPanel().getIdCanvas().isManuallyAdjusted());
+
+    Jalview2XML jv2xml = new jalview.project.Jalview2XML(false);
+    tempfile.delete();
+    jv2xml.saveState(tempfile);
+    assertTrue(jv2xml.errorMessage == null,
+            "Failed to save dummy project with PCA: test broken");
+    af = null;
+    // load again.
+    Desktop.instance.closeAll_actionPerformed(null);
+    af = new FileLoader().LoadFileWaitTillLoaded(
+            tempfile.getCanonicalPath(), DataSourceType.FILE);
+    assertTrue(
+            af.alignPanel.getIdPanel().getIdCanvas().isManuallyAdjusted());
+    assertEquals(af.alignPanel.getAlignViewport().getIdWidth(), 100,
+            "New project exported and import should have adjusted ID width");
+
+    af.alignPanel.getAlignViewport().setIdWidth(100);
+    af.alignPanel.updateLayout();
+    assertTrue(
+            af.alignPanel.getIdPanel().getIdCanvas().isManuallyAdjusted());
+
+    // now make it autoadjusted
+    af.alignPanel.getAlignViewport().setIdWidth(-1);
+    af.alignPanel.getIdPanel().getIdCanvas().setManuallyAdjusted(false);
+    af.alignPanel.updateLayout();
+    assertFalse(
+            af.alignPanel.getIdPanel().getIdCanvas().isManuallyAdjusted());
+    assertTrue(af.alignPanel.getAlignViewport().getIdWidth() > -1,
+            "New project exported and import should have adjusted ID width");
+
+    jv2xml = new jalview.project.Jalview2XML(false);
+    tempfile.delete();
+    jv2xml.saveState(tempfile);
+    assertTrue(jv2xml.errorMessage == null,
+            "Failed to save dummy project with PCA: test broken");
+    af = null;
+    // load again.
+    Desktop.instance.closeAll_actionPerformed(null);
+    af = new FileLoader().LoadFileWaitTillLoaded(
+            tempfile.getCanonicalPath(), DataSourceType.FILE);
+    assertFalse(
+            af.alignPanel.getIdPanel().getIdCanvas().isManuallyAdjusted());
+    assertTrue(af.alignPanel.getAlignViewport().getIdWidth() > -1,
+            "New project exported and import should have adjusted ID width");
   }
 
 }