Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 081f446..33a54e8 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -1332,15 +1332,19 @@ public class AlignmentUtils
           Collection<String> types, List<SequenceI> forSequences,
           boolean anyType, boolean doShow)
   {
-    for (AlignmentAnnotation aa : al.getAlignmentAnnotation())
+    AlignmentAnnotation[] anns = al.getAlignmentAnnotation();
+    if (anns != null)
     {
-      if (anyType || types.contains(aa.label))
+      for (AlignmentAnnotation aa : anns)
       {
-        if ((aa.sequenceRef != null)
-                && (forSequences == null || forSequences
-                        .contains(aa.sequenceRef)))
+        if (anyType || types.contains(aa.label))
         {
-          aa.visible = doShow;
+          if ((aa.sequenceRef != null)
+                  && (forSequences == null || forSequences
+                          .contains(aa.sequenceRef)))
+          {
+            aa.visible = doShow;
+          }
         }
       }
     }

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index bfbc969..133aab4 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -5960,8 +5960,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void setAnnotationsVisibility(boolean visible,
           boolean forSequences, boolean forAlignment)
   {
-    for (AlignmentAnnotation aa : alignPanel.getAlignment()
-            .getAlignmentAnnotation())
+    AlignmentAnnotation[] anns = alignPanel.getAlignment()
+            .getAlignmentAnnotation();
+    if (anns == null)
+    {
+      return;
+    }
+    for (AlignmentAnnotation aa : anns)
     {
       /*
        * don't display non-positional annotations on an alignment

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 8b3aa98..d738882 100755 (executable)
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -1760,6 +1760,10 @@ public class AnnotationFile
    */
   public String printCSVAnnotations(AlignmentAnnotation[] annotations)
   {
+    if (annotations == null)
+    {
+      return "";
+    }
     StringBuffer sp = new StringBuffer();
     for (int i = 0; i < annotations.length; i++)
     {

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index 36980f8..3cda444 100644 (file)
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -744,11 +744,14 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     fr = avpanel.cloneFeatureRenderer();
 
     // Add non auto calculated annotation to AlignFile
-    for (AlignmentAnnotation annot : annots)
+    if (annots != null)
     {
-      if (annot != null && !annot.autoCalculated)
+      for (AlignmentAnnotation annot : annots)
       {
-        annotations.add(annot);
+        if (annot != null && !annot.autoCalculated)
+        {
+          annotations.add(annot);
+        }
       }
     }
     globalColourScheme = ColourSchemeProperty.getColourName(viewport

diff --git a/src/jalview/schemes/FeatureColour.java b/src/jalview/schemes/FeatureColour.java
index 213868b..bdc70c9 100644 (file)
--- a/src/jalview/schemes/FeatureColour.java
+++ b/src/jalview/schemes/FeatureColour.java
@@ -317,6 +317,7 @@ public class FeatureColour implements FeatureColourI
    */
   public FeatureColour(FeatureColour fc)
   {
+    graduatedColour = fc.graduatedColour;
     colour = fc.colour;
     minColour = fc.minColour;
     maxColour = fc.maxColour;

diff --git a/src/jalview/schemes/RNAHelicesColour.java b/src/jalview/schemes/RNAHelicesColour.java
index d17f510..9729a83 100644 (file)
--- a/src/jalview/schemes/RNAHelicesColour.java
+++ b/src/jalview/schemes/RNAHelicesColour.java
@@ -91,6 +91,10 @@ public class RNAHelicesColour extends ResidueColourScheme
     // This loop will find the first rna structure annotation by which to colour
     // the sequences.
     AlignmentAnnotation[] annotations = alignment.getAlignmentAnnotation();
+    if (annotations == null)
+    {
+      return;
+    }
     for (int i = 0; i < annotations.length; i++)
     {
 

diff --git a/src/jalview/schemes/RNAHelicesColourChooser.java b/src/jalview/schemes/RNAHelicesColourChooser.java
index 1a13bbe..b1b3c5a 100644 (file)
--- a/src/jalview/schemes/RNAHelicesColourChooser.java
+++ b/src/jalview/schemes/RNAHelicesColourChooser.java
@@ -22,6 +22,7 @@ package jalview.schemes;
 
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.SequenceGroup;
 
 import java.awt.event.ActionEvent;
@@ -77,16 +78,20 @@ public class RNAHelicesColourChooser
     adjusting = true;
     Vector list = new Vector();
     int index = 1;
-    for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
+    AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
+    if (anns != null)
     {
-      String label = av.getAlignment().getAlignmentAnnotation()[i].label;
-      if (!list.contains(label))
+      for (int i = 0; i < anns.length; i++)
       {
-        list.addElement(label);
-      }
-      else
-      {
-        list.addElement(label + "_" + (index++));
+        String label = anns[i].label;
+        if (!list.contains(label))
+        {
+          list.addElement(label);
+        }
+        else
+        {
+          list.addElement(label + "_" + (index++));
+        }
       }
     }
 

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 0f6d66b..91ee3c1 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -1420,11 +1420,15 @@ public abstract class AlignmentViewport implements AlignViewportI,
   protected void setSequenceAnnotationsVisible(SequenceI sequenceI,
           boolean visible)
   {
-    for (AlignmentAnnotation ann : alignment.getAlignmentAnnotation())
+    AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
+    if (anns != null)
     {
-      if (ann.sequenceRef == sequenceI)
+      for (AlignmentAnnotation ann : anns)
       {
-        ann.visible = visible;
+        if (ann.sequenceRef == sequenceI)
+        {
+          ann.visible = visible;
+        }
       }
     }
   }

diff --git a/src/jalview/workers/StrucConsensusThread.java b/src/jalview/workers/StrucConsensusThread.java
index 3483dac..4249112 100644 (file)
--- a/src/jalview/workers/StrucConsensusThread.java
+++ b/src/jalview/workers/StrucConsensusThread.java
@@ -94,12 +94,15 @@ public class StrucConsensusThread extends AlignCalcWorker
               .getAlignmentAnnotation();
       AlignmentAnnotation rnaStruc = null;
       // select rna struct to use for calculation
-      for (int i = 0; i < aa.length; i++)
+      if (aa != null)
       {
-        if (aa[i].visible && aa[i].isRNA() && aa[i].isValidStruc())
+        for (int i = 0; i < aa.length; i++)
         {
-          rnaStruc = aa[i];
-          break;
+          if (aa[i].visible && aa[i].isRNA() && aa[i].isValidStruc())
+          {
+            rnaStruc = aa[i];
+            break;
+          }
         }
       }
       // check to see if its valid

diff --git a/test/jalview/schemes/FeatureColourTest.java b/test/jalview/schemes/FeatureColourTest.java
index 9b1bd73..e13f542 100644 (file)
--- a/test/jalview/schemes/FeatureColourTest.java
+++ b/test/jalview/schemes/FeatureColourTest.java
@@ -15,6 +15,44 @@ import org.testng.annotations.Test;
 public class FeatureColourTest
 {
   @Test(groups = { "Functional" })
+  public void testCopyConstructor()
+  {
+    /*
+     * plain colour
+     */
+    FeatureColour fc = new FeatureColour(Color.RED);
+    FeatureColour fc1 = new FeatureColour(fc);
+    assertTrue(fc1.getColour().equals(Color.RED));
+    assertFalse(fc1.isGraduatedColour());
+    assertFalse(fc1.isColourByLabel());
+
+    /*
+     * min-max colour
+     */
+    fc = new FeatureColour(Color.gray, Color.black, 10f, 20f);
+    fc.setAboveThreshold(true);
+    fc.setThreshold(12f);
+    fc1 = new FeatureColour(fc);
+    assertTrue(fc1.isGraduatedColour());
+    assertFalse(fc1.isColourByLabel());
+    assertTrue(fc1.isAboveThreshold());
+    assertEquals(12f, fc1.getThreshold());
+    assertEquals(Color.gray, fc1.getMinColour());
+    assertEquals(Color.black, fc1.getMaxColour());
+    assertEquals(10f, fc1.getMin());
+    assertEquals(20f, fc1.getMax());
+
+    /*
+     * colour by label
+     */
+    fc = new FeatureColour();
+    fc.setColourByLabel(true);
+    fc1 = new FeatureColour(fc);
+    assertTrue(fc1.isColourByLabel());
+    assertFalse(fc1.isGraduatedColour());
+  }
+
+  @Test(groups = { "Functional" })
   public void testIsColored_simpleColour()
   {
     FeatureColour fc = new FeatureColour(Color.RED);
@@ -297,5 +335,10 @@ public class FeatureColourTest
     assertEquals(Color.GREEN, fc.getMaxColour());
     assertEquals(10f, fc.getMin());
     assertEquals(20f, fc.getMax());
+
+    descriptor = String
+            .format("blue|255,0,255|absolute|20.0|95.0|below|66.0");
+    fc = FeatureColour.parseJalviewFeatureColour(descriptor);
+    assertTrue(fc.isGraduatedColour());
   }
 }