git://source.jalview.org / jalview.git / blobdiff
? search:
summary | shortlog | log | commit | commitdiff | tree
raw | inline | side by side
Merge branch 'develop' into patch/JAL-4281_idwidthandannotHeight_in_project
[jalview.git] / test / jalview / project / Jalview2xmlTests.java
diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index cbbd0dc..76c5266 100644 (file)
--- a/test/jalview/project/Jalview2xmlTests.java
+++ b/test/jalview/project/Jalview2xmlTests.java
@@ -67,6 +67,7 @@ import jalview.datamodel.HiddenSequences;
 import jalview.datamodel.Mapping;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.PDBEntry.Type;
+import jalview.datamodel.Sequence;
 import jalview.datamodel.Sequence.DBModList;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceFeature;
@@ -288,12 +289,12 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   @Test(groups = { "Functional" })
   public void gatherViewsHere() throws Exception
   {
-    int origCount = Desktop.getAlignFrames() == null ? 0
-            : Desktop.getAlignFrames().length;
+    int origCount = Desktop.getDesktopAlignFrames() == null ? 0
+            : Desktop.getDesktopAlignFrames().length;
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
     assertNotNull(af, "Didn't read in the example file correctly.");
-    assertTrue(Desktop.getAlignFrames().length == 1 + origCount,
+    assertTrue(Desktop.getDesktopAlignFrames().length == 1 + origCount,
             "Didn't gather the views in the example file.");
 
   }
@@ -431,7 +432,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
 
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/exampleFile_2_7.jar", DataSourceType.FILE);
-    Assert.assertEquals(Desktop.getAlignFrames().length, 1);
+    Assert.assertEquals(Desktop.getDesktopAlignFrames().length, 1);
     String afid = af.getViewport().getSequenceSetId();
 
     // check FileLoader returned a reference to the one alignFrame that is
@@ -441,8 +442,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
 
     Desktop.explodeViews(af);
 
-    int oldviews = Desktop.getAlignFrames().length;
-    Assert.assertEquals(Desktop.getAlignFrames().length,
+    int oldviews = Desktop.getDesktopAlignFrames().length;
+    Assert.assertEquals(Desktop.getDesktopAlignFrames().length,
             Desktop.getAlignmentPanels(afid).length);
     File tfile = File.createTempFile("testStoreAndRecoverExpanded", ".jvp");
     try
@@ -456,14 +457,14 @@ public class Jalview2xmlTests extends Jalview2xmlBase
       Assert.fail("Didn't save the expanded view state", e);
     }
     Desktop.instance.closeAll_actionPerformed(null);
-    if (Desktop.getAlignFrames() != null)
+    if (Desktop.getDesktopAlignFrames() != null)
     {
-      Assert.assertEquals(Desktop.getAlignFrames().length, 0);
+      Assert.assertEquals(Desktop.getDesktopAlignFrames().length, 0);
     }
     af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
             DataSourceType.FILE);
     Assert.assertNotNull(af);
-    Assert.assertEquals(Desktop.getAlignFrames().length,
+    Assert.assertEquals(Desktop.getDesktopAlignFrames().length,
             Desktop.getAlignmentPanels(
                     af.getViewport().getSequenceSetId()).length);
     Assert.assertEquals(Desktop
@@ -520,9 +521,9 @@ public class Jalview2xmlTests extends Jalview2xmlBase
       Assert.fail("Didn't save the expanded view state", e);
     }
     Desktop.instance.closeAll_actionPerformed(null);
-    if (Desktop.getAlignFrames() != null)
+    if (Desktop.getDesktopAlignFrames() != null)
     {
-      Assert.assertEquals(Desktop.getAlignFrames().length, 0);
+      Assert.assertEquals(Desktop.getDesktopAlignFrames().length, 0);
     }
 
     af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
@@ -699,9 +700,9 @@ public class Jalview2xmlTests extends Jalview2xmlBase
       Assert.fail("Didn't save the expanded view state", e);
     }
     Desktop.instance.closeAll_actionPerformed(null);
-    if (Desktop.getAlignFrames() != null)
+    if (Desktop.getDesktopAlignFrames() != null)
     {
-      Assert.assertEquals(Desktop.getAlignFrames().length, 0);
+      Assert.assertEquals(Desktop.getDesktopAlignFrames().length, 0);
     }
 
     af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
@@ -793,9 +794,9 @@ public class Jalview2xmlTests extends Jalview2xmlBase
       Assert.fail("Didn't save the state", e);
     }
     Desktop.instance.closeAll_actionPerformed(null);
-    if (Desktop.getAlignFrames() != null)
+    if (Desktop.getDesktopAlignFrames() != null)
     {
-      Assert.assertEquals(Desktop.getAlignFrames().length, 0);
+      Assert.assertEquals(Desktop.getDesktopAlignFrames().length, 0);
     }
 
     AlignFrame restoredFrame = new FileLoader().LoadFileWaitTillLoaded(
@@ -1218,7 +1219,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     assertNotNull(af);
 
     AlignmentI ds = null;
-    for (AlignFrame alignFrame : Desktop.getAlignFrames())
+    for (AlignFrame alignFrame : Desktop.getDesktopAlignFrames())
     {
       if (ds == null)
       {
@@ -1547,6 +1548,44 @@ 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)
+    {
+      sq.setSequence(sq.getSequenceAsString()+'Q');
+    }
+    float[][] paevals = new float[i][i];
+    for (i = imax - 1; i >= 0; i--)
+    {
+      for (int j = 0; j <= i; j++)
+      {
+        paevals[i][j] = ((i - j < 2)
+                || ((i > 1 && i < 5) && (j > 1 && i < 5))) ? 1 : 0f;
+        paevals[j][i] = -paevals[i][j];
+      }
+    }
+    PAEContactMatrix dummyMat = new PAEContactMatrix(sq, paevals);
+    String content = ContactMatrix.contactToFloatString(dummyMat);
+    Assert.assertTrue(content.contains("\t1.")); // at least one element must be
+                                                 // 1
+    float[][] vals = ContactMatrix.fromFloatStringToContacts(content,
+            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 (int j=0;j<imax;j++)
+      {
+        assertEquals(vals[i][j],paevals[i][j]);
+      }
+    }
+  }
+  @Test(groups = { "Functional" })
   public void testPAEsaveRestore() throws Exception
   {
     Desktop.instance.closeAll_actionPerformed(null);
@@ -1699,4 +1738,67 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     
   }
 
+  @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.");
+      assertEquals(af.alignPanel.getAlignViewport().getIdWidth(), 144,
+              "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");
+  }
+
 }