From 0a5ce6145bb76fc7eb8a5cc2670e20453fbedd29 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Wed, 2 Nov 2016 10:05:20 +0000 Subject: [PATCH] JAL-98 Profile and ResidueCount moved from analysis to datamodel --- src/jalview/analysis/AAFrequency.java | 4 +++- src/jalview/analysis/Conservation.java | 3 ++- src/jalview/api/AlignViewportI.java | 2 +- src/jalview/{analysis => datamodel}/Profile.java | 2 +- src/jalview/{analysis => datamodel}/ResidueCount.java | 2 +- src/jalview/datamodel/SequenceGroup.java | 1 - src/jalview/renderer/AnnotationRenderer.java | 2 +- src/jalview/schemes/ColourSchemeI.java | 2 +- src/jalview/schemes/FollowerColourScheme.java | 2 +- src/jalview/schemes/ResidueColourScheme.java | 2 +- src/jalview/viewmodel/AlignmentViewport.java | 2 +- src/jalview/workers/ConsensusThread.java | 2 +- test/jalview/analysis/AAFrequencyTest.java | 1 + test/jalview/{analysis => datamodel}/ResidueCountTest.java | 5 +++-- test/jalview/schemes/ResidueColourSchemeTest.java | 2 +- 15 files changed, 19 insertions(+), 15 deletions(-) rename src/jalview/{analysis => datamodel}/Profile.java (99%) rename src/jalview/{analysis => datamodel}/ResidueCount.java (99%) rename test/jalview/{analysis => datamodel}/ResidueCountTest.java (98%) diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java index 61e11c4..30d5373 100755 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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; -- 1.7.10.2