JAL-98 Profile and ResidueCount moved from analysis to datamodel

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 61e11c4..30d5373 100755 (executable)
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -20,12 +20,14 @@
  */
 package jalview.analysis;
 
-import jalview.analysis.ResidueCount.SymbolCounts;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.Profile;
+import jalview.datamodel.ResidueCount;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.ResidueCount.SymbolCounts;
 import jalview.ext.android.SparseIntArray;
 import jalview.util.Comparison;
 import jalview.util.Format;

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index 027a096..7e72dcd 100755 (executable)
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -20,11 +20,12 @@
  */
 package jalview.analysis;
 
-import jalview.analysis.ResidueCount.SymbolCounts;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.ResidueCount;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.ResidueCount.SymbolCounts;
 import jalview.schemes.ResidueProperties;
 import jalview.util.Comparison;
 

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 70463e7..32f9ecd 100644 (file)
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -21,12 +21,12 @@
 package jalview.api;
 
 import jalview.analysis.Conservation;
-import jalview.analysis.Profile;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.CigarArray;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.Profile;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;

diff --git a/src/jalview/analysis/Profile.java b/src/jalview/datamodel/Profile.java
similarity index 99%
rename from src/jalview/analysis/Profile.java
rename to src/jalview/datamodel/Profile.java
index d94d031..2951e9e 100644 (file)
--- a/src/jalview/analysis/Profile.java
+++ b/src/jalview/datamodel/Profile.java
@@ -1,4 +1,4 @@
-package jalview.analysis;
+package jalview.datamodel;
 
 
 /**

diff --git a/src/jalview/analysis/ResidueCount.java b/src/jalview/datamodel/ResidueCount.java
similarity index 99%
rename from src/jalview/analysis/ResidueCount.java
rename to src/jalview/datamodel/ResidueCount.java
index 351c927..0d0348c 100644 (file)
--- a/src/jalview/analysis/ResidueCount.java
+++ b/src/jalview/datamodel/ResidueCount.java
@@ -1,4 +1,4 @@
-package jalview.analysis;
+package jalview.datamodel;
 
 import jalview.util.Comparison;
 import jalview.util.Format;

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 98fd8f2..a92eade 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -22,7 +22,6 @@ package jalview.datamodel;
 
 import jalview.analysis.AAFrequency;
 import jalview.analysis.Conservation;
-import jalview.analysis.Profile;
 import jalview.schemes.ColourSchemeI;
 
 import java.awt.Color;

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index ed758c5..adcedcb 100644 (file)
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -22,13 +22,13 @@ package jalview.renderer;
 
 import jalview.analysis.AAFrequency;
 import jalview.analysis.CodingUtils;
-import jalview.analysis.Profile;
 import jalview.analysis.Rna;
 import jalview.analysis.StructureFrequency;
 import jalview.api.AlignViewportI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.Profile;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ResidueProperties;
 import jalview.util.Platform;

diff --git a/src/jalview/schemes/ColourSchemeI.java b/src/jalview/schemes/ColourSchemeI.java
index 165ece9..54c8c99 100755 (executable)
--- a/src/jalview/schemes/ColourSchemeI.java
+++ b/src/jalview/schemes/ColourSchemeI.java
@@ -20,8 +20,8 @@
  */
 package jalview.schemes;
 
-import jalview.analysis.Profile;
 import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.Profile;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
 

diff --git a/src/jalview/schemes/FollowerColourScheme.java b/src/jalview/schemes/FollowerColourScheme.java
index 0dcf960..e1c343c 100644 (file)
--- a/src/jalview/schemes/FollowerColourScheme.java
+++ b/src/jalview/schemes/FollowerColourScheme.java
@@ -21,7 +21,7 @@
 package jalview.schemes;
 
 import jalview.analysis.Conservation;
-import jalview.analysis.Profile;
+import jalview.datamodel.Profile;
 
 /**
  * Colourscheme that takes its colours from some other colourscheme

diff --git a/src/jalview/schemes/ResidueColourScheme.java b/src/jalview/schemes/ResidueColourScheme.java
index a15ca20..c9abb0e 100755 (executable)
--- a/src/jalview/schemes/ResidueColourScheme.java
+++ b/src/jalview/schemes/ResidueColourScheme.java
@@ -21,8 +21,8 @@
 package jalview.schemes;
 
 import jalview.analysis.Conservation;
-import jalview.analysis.Profile;
 import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.Profile;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
 import jalview.util.ColorUtils;

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index c01be4e..54215e1 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -22,7 +22,6 @@ package jalview.viewmodel;
 
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.analysis.Conservation;
-import jalview.analysis.Profile;
 import jalview.api.AlignCalcManagerI;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
@@ -37,6 +36,7 @@ import jalview.datamodel.Annotation;
 import jalview.datamodel.CigarArray;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.HiddenSequences;
+import jalview.datamodel.Profile;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceCollectionI;

diff --git a/src/jalview/workers/ConsensusThread.java b/src/jalview/workers/ConsensusThread.java
index c88a24a..4bd8c48 100644 (file)
--- a/src/jalview/workers/ConsensusThread.java
+++ b/src/jalview/workers/ConsensusThread.java
@@ -21,12 +21,12 @@
 package jalview.workers;
 
 import jalview.analysis.AAFrequency;
-import jalview.analysis.Profile;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.Profile;
 import jalview.datamodel.SequenceI;
 import jalview.schemes.ColourSchemeI;
 

diff --git a/test/jalview/analysis/AAFrequencyTest.java b/test/jalview/analysis/AAFrequencyTest.java
index 0ddbddc..bb3510a 100644 (file)
--- a/test/jalview/analysis/AAFrequencyTest.java
+++ b/test/jalview/analysis/AAFrequencyTest.java
@@ -25,6 +25,7 @@ import static org.testng.AssertJUnit.assertNull;
 
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.Profile;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 

diff --git a/test/jalview/analysis/ResidueCountTest.java b/test/jalview/datamodel/ResidueCountTest.java
similarity index 98%
rename from test/jalview/analysis/ResidueCountTest.java
rename to test/jalview/datamodel/ResidueCountTest.java
index 4a71f89..e879e33 100644 (file)
--- a/test/jalview/analysis/ResidueCountTest.java
+++ b/test/jalview/datamodel/ResidueCountTest.java
@@ -1,10 +1,11 @@
-package jalview.analysis;
+package jalview.datamodel;
 
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertFalse;
 import static org.testng.Assert.assertTrue;
 
-import jalview.analysis.ResidueCount.SymbolCounts;
+import jalview.datamodel.ResidueCount;
+import jalview.datamodel.ResidueCount.SymbolCounts;
 
 import org.junit.Assert;
 import org.testng.annotations.Test;

diff --git a/test/jalview/schemes/ResidueColourSchemeTest.java b/test/jalview/schemes/ResidueColourSchemeTest.java
index 8173dd1..dcd9f94 100644 (file)
--- a/test/jalview/schemes/ResidueColourSchemeTest.java
+++ b/test/jalview/schemes/ResidueColourSchemeTest.java
@@ -4,7 +4,7 @@ import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertTrue;
 
-import jalview.analysis.Profile;
+import jalview.datamodel.Profile;
 
 import java.awt.Color;