JAL-2939 pull up set/IsNormalise[HMM]SequenceLogo

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index b0d6f85..753e972 100644 (file)
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -299,17 +299,6 @@ public class AlignViewport extends AlignmentViewport
             .getStructureSelectionManager(applet);
   }
 
-  @Override
-  public boolean isNormaliseSequenceLogo()
-  {
-    return normaliseSequenceLogo;
-  }
-
-  public void setNormaliseSequenceLogo(boolean state)
-  {
-    normaliseSequenceLogo = state;
-  }
-
   /**
    * 
    * @return true if alignment characters should be displayed
@@ -408,10 +397,4 @@ public class AlignViewport extends AlignmentViewport
     // TODO implement for applet
   }
 
-  @Override
-  public boolean isNormaliseHMMSequenceLogo()
-  {
-    return normaliseHMMSequenceLogo;
-  }
-
 }

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 96fea6e..63cbfbd 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -35,7 +35,6 @@ import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceGroup;
@@ -57,11 +56,9 @@ import java.awt.Dimension;
 import java.awt.Font;
 import java.awt.FontMetrics;
 import java.awt.Rectangle;
-import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.Iterator;
 import java.util.List;
-import java.util.Vector;
 
 import javax.swing.JInternalFrame;
 
@@ -588,23 +585,6 @@ public class AlignViewport extends AlignmentViewport
             .getStructureSelectionManager(Desktop.instance);
   }
 
-  @Override
-  public boolean isNormaliseSequenceLogo()
-  {
-    return normaliseSequenceLogo;
-  }
-
-
-  public void setNormaliseSequenceLogo(boolean state)
-  {
-    normaliseSequenceLogo = state;
-  }
-
-  public void setNormaliseHMMSequenceLogo(boolean state)
-  {
-    normaliseHMMSequenceLogo = state;
-  }
-
   /**
    * 
    * @return true if alignment characters should be displayed
@@ -1045,10 +1025,4 @@ public class AlignViewport extends AlignmentViewport
     fr.setTransparency(featureSettings.getTransparency());
   }
 
-  @Override
-  public boolean isNormaliseHMMSequenceLogo()
-  {
-    return normaliseHMMSequenceLogo;
-  }
-
 }

diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java
index f674c7e..eaaf0a5 100644 (file)
--- a/src/jalview/gui/CalculationChooser.java
+++ b/src/jalview/gui/CalculationChooser.java
@@ -23,10 +23,12 @@ package jalview.gui;
 import jalview.analysis.TreeBuilder;
 import jalview.analysis.scoremodels.ScoreModels;
 import jalview.analysis.scoremodels.SimilarityParams;
+import jalview.api.AlignViewportI;
 import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.SimilarityParamsI;
 import jalview.datamodel.SequenceGroup;
 import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
@@ -103,7 +105,7 @@ public class CalculationChooser extends JPanel
 
   final ComboBoxTooltipRenderer renderer = new ComboBoxTooltipRenderer();
 
-  List<String> tips = new ArrayList<String>();
+  List<String> tips = new ArrayList<>();
 
   /*
    * the most recently opened PCA results panel
@@ -375,7 +377,7 @@ public class CalculationChooser extends JPanel
    */
   protected JComboBox<String> buildModelOptionsList()
   {
-    final JComboBox<String> scoreModelsCombo = new JComboBox<String>();
+    final JComboBox<String> scoreModelsCombo = new JComboBox<>();
     scoreModelsCombo.setRenderer(renderer);
 
     /*
@@ -418,7 +420,7 @@ public class CalculationChooser extends JPanel
   {
     Object curSel = comboBox.getSelectedItem();
     toolTips.clear();
-    DefaultComboBoxModel<String> model = new DefaultComboBoxModel<String>();
+    DefaultComboBoxModel<String> model = new DefaultComboBoxModel<>();
 
     /*
      * now we can actually add entries to the combobox,
@@ -492,7 +494,7 @@ public class CalculationChooser extends JPanel
      * gui validation shouldn't allow insufficient sequences here, but leave
      * this check in in case this method gets exposed programmatically in future
      */
-    AlignViewport viewport = af.getViewport();
+    AlignViewportI viewport = af.getViewport();
     SequenceGroup sg = viewport.getSelectionGroup();
     if (sg != null && sg.getSize() < MIN_TREE_SELECTION)
     {
@@ -519,7 +521,7 @@ public class CalculationChooser extends JPanel
    */
   protected void openPcaPanel(String modelName, SimilarityParamsI params)
   {
-    AlignViewport viewport = af.getViewport();
+    AlignViewportI viewport = af.getViewport();
 
     /*
      * gui validation shouldn't allow insufficient sequences here, but leave

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 24ed1f7..b26a8af 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -1471,7 +1471,8 @@ public class Desktop extends jalview.jbgui.GDesktop
       return;
     }
 
-    AlignmentViewport source = null, target = null;
+    AlignViewportI source = null;
+    AlignViewportI target = null;
     if (frames[0] instanceof AlignFrame)
     {
       source = ((AlignFrame) frames[0]).getCurrentView();

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 02d54a8..ffedede 100755 (executable)
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.api.AlignViewportI;
 import jalview.bin.Cache;
 import jalview.renderer.OverviewRenderer;
 import jalview.util.MessageManager;
@@ -62,7 +63,7 @@ public class OverviewPanel extends JPanel
 
   private OverviewCanvas oviewCanvas;
 
-  private AlignViewport av;
+  private AlignViewportI av;
 
   private AlignmentPanel ap;
 

diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index d081794..e736a11 100755 (executable)
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -21,13 +21,13 @@
 package jalview.gui;
 
 import jalview.analysis.AlignSeq;
+import jalview.api.AlignViewportI;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.jbgui.GPairwiseAlignPanel;
 import jalview.util.MessageManager;
-import jalview.viewmodel.AlignmentViewport;
 
 import java.awt.event.ActionEvent;
 import java.util.Vector;
@@ -43,7 +43,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
 
   private static final String DASHES = "---------------------\n";
 
-  AlignmentViewport av;
+  AlignViewportI av;
 
   Vector<SequenceI> sequences;
 
@@ -51,14 +51,13 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
    * Creates a new PairwiseAlignPanel object.
    * 
    * @param viewport
-   *          DOCUMENT ME!
    */
-  public PairwiseAlignPanel(AlignmentViewport viewport)
+  public PairwiseAlignPanel(AlignViewportI viewport)
   {
     super();
     this.av = viewport;
 
-    sequences = new Vector<SequenceI>();
+    sequences = new Vector<>();
 
     SequenceGroup selectionGroup = viewport.getSelectionGroup();
     boolean isSelection = selectionGroup != null

diff --git a/src/jalview/gui/SplitFrame.java b/src/jalview/gui/SplitFrame.java
index 5bff407..56d1fac 100644 (file)
--- a/src/jalview/gui/SplitFrame.java
+++ b/src/jalview/gui/SplitFrame.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.api.AlignViewportI;
 import jalview.api.SplitContainerI;
 import jalview.datamodel.AlignmentI;
 import jalview.jbgui.GAlignFrame;
@@ -215,8 +216,8 @@ public class SplitFrame extends GSplitFrame implements SplitContainerI
     topFrame.alignPanel.adjustAnnotationHeight();
     bottomFrame.alignPanel.adjustAnnotationHeight();
 
-    final AlignViewport topViewport = topFrame.viewport;
-    final AlignViewport bottomViewport = bottomFrame.viewport;
+    final AlignViewportI topViewport = topFrame.viewport;
+    final AlignViewportI bottomViewport = bottomFrame.viewport;
     final AlignmentI topAlignment = topViewport.getAlignment();
     final AlignmentI bottomAlignment = bottomViewport.getAlignment();
     boolean topAnnotations = topViewport.isShowAnnotation();

diff --git a/src/jalview/hmmer/HMMBuild.java b/src/jalview/hmmer/HMMBuild.java
index 373c160..97dc59a 100644 (file)
--- a/src/jalview/hmmer/HMMBuild.java
+++ b/src/jalview/hmmer/HMMBuild.java
@@ -8,12 +8,12 @@ import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
-import jalview.gui.AlignViewport;
 import jalview.gui.JvOptionPane;
 import jalview.io.DataSourceType;
 import jalview.io.FileParse;
 import jalview.io.HMMFile;
 import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
 import jalview.ws.params.ArgumentI;
 
 import java.io.File;
@@ -66,7 +66,7 @@ public class HMMBuild extends HmmerCommand
     af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
             msgID);
 
-    AlignViewport viewport = af.getViewport();
+    AlignViewportI viewport = af.getViewport();
     try
     {
       /*

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index ff47484..0f46d5a 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -3076,4 +3076,26 @@ public abstract class AlignmentViewport
   {
     return currentTree;
   }
+
+  @Override
+  public boolean isNormaliseSequenceLogo()
+  {
+    return normaliseSequenceLogo;
+  }
+
+  public void setNormaliseSequenceLogo(boolean state)
+  {
+    normaliseSequenceLogo = state;
+  }
+
+  @Override
+  public boolean isNormaliseHMMSequenceLogo()
+  {
+    return normaliseHMMSequenceLogo;
+  }
+
+  public void setNormaliseHMMSequenceLogo(boolean state)
+  {
+    normaliseHMMSequenceLogo = state;
+  }
 }

diff --git a/test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java b/test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java
index 16ca70d..a1623f6 100644 (file)
--- a/test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java
+++ b/test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java
@@ -23,6 +23,7 @@ package jalview.analysis.scoremodels;
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertTrue;
 
+import jalview.api.AlignViewportI;
 import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.SimilarityParamsI;
 import jalview.datamodel.Alignment;
@@ -32,7 +33,6 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
-import jalview.gui.AlignViewport;
 import jalview.gui.JvOptionPane;
 import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
@@ -280,7 +280,7 @@ public class FeatureDistanceModelTest
   public void testFindDistances_withParams()
   {
     AlignFrame af = setupAlignmentView();
-    AlignViewport viewport = af.getViewport();
+    AlignViewportI viewport = af.getViewport();
     AlignmentView view = viewport.getAlignmentView(false);
 
     ScoreModelI sm = new FeatureDistanceModel();

diff --git a/test/jalview/datamodel/AlignmentViewTest.java b/test/jalview/datamodel/AlignmentViewTest.java
index b201c7e..9be344c 100644 (file)
--- a/test/jalview/datamodel/AlignmentViewTest.java
+++ b/test/jalview/datamodel/AlignmentViewTest.java
@@ -23,10 +23,10 @@ package jalview.datamodel;
 import static org.testng.Assert.assertEquals;
 
 import jalview.gui.AlignFrame;
-import jalview.gui.AlignViewport;
 import jalview.gui.JvOptionPane;
 import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
+import jalview.viewmodel.AlignmentViewport;
 
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
@@ -60,7 +60,7 @@ public class AlignmentViewTest
   {
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             ">s1\n0123456789\n", DataSourceType.PASTE);
-    AlignViewport av = af.getViewport();
+    AlignmentViewport av = af.getViewport();
     AlignmentView view = av.getAlignmentView(true);
 
     /*

diff --git a/test/jalview/datamodel/HiddenSequencesTest.java b/test/jalview/datamodel/HiddenSequencesTest.java
index 11b993d..efd71e6 100644 (file)
--- a/test/jalview/datamodel/HiddenSequencesTest.java
+++ b/test/jalview/datamodel/HiddenSequencesTest.java
@@ -31,6 +31,7 @@ import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
 
 import jalview.gui.AlignViewport;
 import jalview.gui.JvOptionPane;
+import jalview.viewmodel.AlignmentViewport;
 
 import java.util.List;
 
@@ -487,7 +488,7 @@ public class HiddenSequencesTest
      * represent seqs 2-4 with seq3
      * this hides seq2 and seq4 but not seq3
      */
-    AlignViewport av = new AlignViewport(al);
+    AlignmentViewport av = new AlignViewport(al);
     SequenceGroup sg = new SequenceGroup();
     sg.addSequence(seqs[1], false);
     sg.addSequence(seqs[2], false);

diff --git a/test/jalview/gui/AlignFrameTest.java b/test/jalview/gui/AlignFrameTest.java
index b0aaab9..0f15ce4 100644 (file)
--- a/test/jalview/gui/AlignFrameTest.java
+++ b/test/jalview/gui/AlignFrameTest.java
@@ -26,6 +26,7 @@ import static org.testng.Assert.assertNotSame;
 import static org.testng.Assert.assertSame;
 import static org.testng.Assert.assertTrue;
 
+import jalview.api.AlignViewportI;
 import jalview.api.FeatureColourI;
 import jalview.bin.Cache;
 import jalview.bin.Jalview;
@@ -47,6 +48,7 @@ import jalview.schemes.JalviewColourScheme;
 import jalview.schemes.StrandColourScheme;
 import jalview.schemes.TurnColourScheme;
 import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
 
 import java.awt.Color;
 import java.util.Iterator;
@@ -208,7 +210,7 @@ public class AlignFrameTest
   @Test(groups = "Functional")
   public void testChangeColour_background_groupsAndThresholds()
   {
-    AlignViewport av = af.getViewport();
+    AlignViewportI av = af.getViewport();
     AlignmentI al = av.getAlignment();
 
     /*
@@ -339,7 +341,7 @@ public class AlignFrameTest
   @Test(groups = "Functional")
   public void testColourThresholdActions()
   {
-    AlignViewport av = af.getViewport();
+    AlignViewportI av = af.getViewport();
     AlignmentI al = av.getAlignment();
 
     /*
@@ -508,7 +510,7 @@ public class AlignFrameTest
   @Test(groups = "Functional")
   public void testNewView_colourThresholds()
   {
-    AlignViewport av = af.getViewport();
+    AlignViewportI av = af.getViewport();
     AlignmentI al = av.getAlignment();
 
     /*
@@ -572,7 +574,7 @@ public class AlignFrameTest
      */
     af.newView_actionPerformed(null);
     assertEquals(af.alignPanel.getViewName(), "View 1");
-    AlignViewport av2 = af.getViewport();
+    AlignmentViewport av2 = af.getViewport();
     assertNotSame(av, av2);
     assertSame(av2, af.alignPanel.av);
     rs = av2.getResidueShading();

diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java
index f0120d6..6ab2622 100644 (file)
--- a/test/jalview/gui/AlignViewportTest.java
+++ b/test/jalview/gui/AlignViewportTest.java
@@ -26,6 +26,7 @@ import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.api.AlignViewportI;
 import jalview.bin.Cache;
 import jalview.bin.Jalview;
 import jalview.datamodel.AlignedCodonFrame;
@@ -33,8 +34,6 @@ import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.PDBEntry.Type;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.Sequence;
@@ -46,6 +45,7 @@ import jalview.schemes.ColourSchemeI;
 import jalview.schemes.PIDColourScheme;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MapList;
+import jalview.viewmodel.AlignmentViewport;
 import jalview.viewmodel.ViewportRanges;
 
 import java.util.ArrayList;
@@ -68,7 +68,7 @@ public class AlignViewportTest
 
   AlignmentI al;
 
-  AlignViewport testee;
+  AlignmentViewport testee;
 
   @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
@@ -355,7 +355,7 @@ public class AlignViewportTest
   {
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/uniref50.fa", DataSourceType.FILE);
-    AlignViewport av = af.getViewport();
+    AlignViewportI av = af.getViewport();
     SequenceGroup sg1 = new SequenceGroup();
     SequenceGroup sg2 = new SequenceGroup();
     SequenceGroup sg3 = new SequenceGroup();
@@ -384,7 +384,7 @@ public class AlignViewportTest
     jalview.bin.Cache.setProperty("SHOW_OCCUPANCY", Boolean.FALSE.toString());
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/uniref50.fa", DataSourceType.FILE);
-    AlignViewport av = af.getViewport();
+    AlignViewportI av = af.getViewport();
     Assert.assertNull(av.getOccupancyAnnotation(), "Preference did not disable occupancy row.");
     int c = 0;
     for (AlignmentAnnotation aa : av.getAlignment().findAnnotations(null,
@@ -423,7 +423,7 @@ public class AlignViewportTest
     String fasta = ">s1\nA-C\n>s2\nA-C\n>s3\nA-D\n>s4\n--D\n";
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(fasta,
             DataSourceType.PASTE);
-    AlignViewport testme = af.getViewport();
+    AlignmentViewport testme = af.getViewport();
     SequenceI cons = testme.getConsensusSeq();
     assertEquals("A-C", cons.getSequenceAsString());
   }

diff --git a/test/jalview/gui/PairwiseAlignmentPanelTest.java b/test/jalview/gui/PairwiseAlignmentPanelTest.java
index 3322ee8..1ea0ba1 100644 (file)
--- a/test/jalview/gui/PairwiseAlignmentPanelTest.java
+++ b/test/jalview/gui/PairwiseAlignmentPanelTest.java
@@ -2,17 +2,19 @@ package jalview.gui;
 
 import static org.testng.Assert.assertEquals;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceGroup;
 import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
+import jalview.viewmodel.AlignmentViewport;
 
 import javax.swing.JTextArea;
 
-import junit.extensions.PA;
-
 import org.testng.annotations.Test;
 
+import junit.extensions.PA;
+
 public class PairwiseAlignmentPanelTest
 {
   @Test(groups = "Functional")
@@ -20,7 +22,7 @@ public class PairwiseAlignmentPanelTest
   {
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/uniref50.fa", DataSourceType.FILE);
-    AlignViewport viewport = af.getViewport();
+    AlignViewportI viewport = af.getViewport();
     AlignmentI al = viewport.getAlignment();
 
     /*
@@ -58,7 +60,7 @@ public class PairwiseAlignmentPanelTest
     String seqs = ">Q93XJ9_SOLTU/23-29\nL-KAISNV\n>FER1_PEA/26-32\nV-TTTKAF\n";
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqs,
             DataSourceType.PASTE);
-    AlignViewport viewport = af.getViewport();
+    AlignViewportI viewport = af.getViewport();
 
     PairwiseAlignPanel testee = new PairwiseAlignPanel(viewport);
 

diff --git a/test/jalview/gui/SequenceRendererTest.java b/test/jalview/gui/SequenceRendererTest.java
index 359377a..d3d6476 100644 (file)
--- a/test/jalview/gui/SequenceRendererTest.java
+++ b/test/jalview/gui/SequenceRendererTest.java
@@ -22,6 +22,7 @@ package jalview.gui;
 
 import static org.testng.Assert.assertEquals;
 
+import jalview.api.AlignViewportI;
 import jalview.bin.Jalview;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
@@ -41,7 +42,7 @@ import org.testng.annotations.Test;
 public class SequenceRendererTest
 {
   AlignmentI al;
-  AlignViewport av;
+  AlignViewportI av;
 
   SequenceI seq1;
 

diff --git a/test/jalview/io/Jalview2xmlTests.java b/test/jalview/io/Jalview2xmlTests.java
index e9e0782..41a6b89 100644 (file)
--- a/test/jalview/io/Jalview2xmlTests.java
+++ b/test/jalview/io/Jalview2xmlTests.java
@@ -44,7 +44,6 @@ import jalview.datamodel.features.FeatureMatcher;
 import jalview.datamodel.features.FeatureMatcherSet;
 import jalview.datamodel.features.FeatureMatcherSetI;
 import jalview.gui.AlignFrame;
-import jalview.gui.AlignViewport;
 import jalview.gui.AlignmentPanel;
 import jalview.gui.Desktop;
 import jalview.gui.FeatureRenderer;
@@ -771,7 +770,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/uniref50.fa", DataSourceType.FILE);
 
-    AlignViewport av = af.getViewport();
+    AlignViewportI av = af.getViewport();
     AlignmentI al = av.getAlignment();
 
     /*

diff --git a/test/jalview/renderer/OverviewResColourFinderTest.java b/test/jalview/renderer/OverviewResColourFinderTest.java
index 1687516..d01e53f 100644 (file)
--- a/test/jalview/renderer/OverviewResColourFinderTest.java
+++ b/test/jalview/renderer/OverviewResColourFinderTest.java
@@ -22,6 +22,7 @@ package jalview.renderer;
 
 import static org.testng.AssertJUnit.assertEquals;
 
+import jalview.api.AlignViewportI;
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
@@ -33,6 +34,7 @@ import jalview.gui.JvOptionPane;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.UserColourScheme;
 import jalview.schemes.ZappoColourScheme;
+import jalview.viewmodel.AlignmentViewport;
 
 import java.awt.Color;
 import java.util.ArrayList;
@@ -56,7 +58,7 @@ public class OverviewResColourFinderTest
   {
     SequenceI seq = new Sequence("name", "MA--TVLGSPRAPAFF");
     AlignmentI al = new Alignment(new SequenceI[] { seq });
-    final AlignViewport av = new AlignViewport(al);
+    final AlignViewportI av = new AlignViewport(al);
     ResidueColourFinder rcf = new OverviewResColourFinder();
 
     // gaps are grey, residues white
@@ -80,7 +82,7 @@ public class OverviewResColourFinderTest
     SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
                                                             // gap
     AlignmentI al = new Alignment(new SequenceI[] { seq });
-    final AlignViewport av = new AlignViewport(al);
+    final AlignViewportI av = new AlignViewport(al);
     ResidueColourFinder rcf = new OverviewResColourFinder();
     av.setGlobalColourScheme(new ZappoColourScheme());
 
@@ -126,7 +128,7 @@ public class OverviewResColourFinderTest
     SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
                                                             // gap
     AlignmentI al = new Alignment(new SequenceI[] { seq });
-    final AlignViewport av = new AlignViewport(al);
+    final AlignViewportI av = new AlignViewport(al);
     ResidueColourFinder rcf = new OverviewResColourFinder();
 
     Color[] newColours = new Color[24];
@@ -179,7 +181,7 @@ public class OverviewResColourFinderTest
     SequenceGroup[] groups = new SequenceGroup[1];
     groups[0] = sg;
     
-    final AlignViewport av = new AlignViewport(al);
+    final AlignViewportI av = new AlignViewport(al);
     ResidueColourFinder rcf = new OverviewResColourFinder();
     
     // G in group specified as magenta in Zappo
@@ -230,8 +232,6 @@ public class OverviewResColourFinderTest
   {
     SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
                                                             // gap
-    AlignmentI al = new Alignment(new SequenceI[] { seq });
-    final AlignViewport av = new AlignViewport(al);
 
     // non-legacy colouring
     ResidueColourFinder rcf = new OverviewResColourFinder();
@@ -269,9 +269,7 @@ public class OverviewResColourFinderTest
 
     // gaps gap colour
     c = rcf.getBoxColour(shader, seq, 3);
-    assertEquals(
-            jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP,
-            c);
+    assertEquals(OverviewResColourFinder.OVERVIEW_DEFAULT_GAP, c);
 
     // non legacy colouring with colour scheme
     rcf = new OverviewResColourFinder(false, Color.blue, Color.red);

diff --git a/test/jalview/renderer/ResidueColourFinderTest.java b/test/jalview/renderer/ResidueColourFinderTest.java
index 81fb2c0..24f653c 100644 (file)
--- a/test/jalview/renderer/ResidueColourFinderTest.java
+++ b/test/jalview/renderer/ResidueColourFinderTest.java
@@ -22,6 +22,7 @@ package jalview.renderer;
 
 import static org.testng.AssertJUnit.assertEquals;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Sequence;
@@ -30,6 +31,7 @@ import jalview.gui.AlignViewport;
 import jalview.gui.JvOptionPane;
 import jalview.schemes.UserColourScheme;
 import jalview.schemes.ZappoColourScheme;
+import jalview.viewmodel.AlignmentViewport;
 
 import java.awt.Color;
 
@@ -51,7 +53,7 @@ public class ResidueColourFinderTest
   {
     SequenceI seq = new Sequence("name", "MATVLGSPRAPAFF"); // FER1_MAIZE...
     AlignmentI al = new Alignment(new SequenceI[] { seq });
-    final AlignViewport av = new AlignViewport(al);
+    final AlignViewportI av = new AlignViewport(al);
     ResidueColourFinder rcf = new ResidueColourFinder();
     av.setGlobalColourScheme(new ZappoColourScheme());
 
@@ -86,7 +88,7 @@ public class ResidueColourFinderTest
   {
     SequenceI seq = new Sequence("name", "MA--TVLGSPRAPAFF");
     AlignmentI al = new Alignment(new SequenceI[] { seq });
-    final AlignViewport av = new AlignViewport(al);
+    final AlignViewportI av = new AlignViewport(al);
     ResidueColourFinder rcf = new ResidueColourFinder();
 
     assertEquals(Color.white,
@@ -109,7 +111,7 @@ public class ResidueColourFinderTest
     SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
                                                             // gap
     AlignmentI al = new Alignment(new SequenceI[] { seq });
-    final AlignViewport av = new AlignViewport(al);
+    final AlignViewportI av = new AlignViewport(al);
     ResidueColourFinder rcf = new ResidueColourFinder();
 
     Color[] newColours = new Color[24];

diff --git a/test/jalview/renderer/ScaleRendererTest.java b/test/jalview/renderer/ScaleRendererTest.java
index 0af67cd..e78fc5a 100644 (file)
--- a/test/jalview/renderer/ScaleRendererTest.java
+++ b/test/jalview/renderer/ScaleRendererTest.java
@@ -6,10 +6,10 @@ import static org.testng.Assert.assertNull;
 import static org.testng.Assert.assertTrue;
 
 import jalview.gui.AlignFrame;
-import jalview.gui.AlignViewport;
 import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
 import jalview.renderer.ScaleRenderer.ScaleMark;
+import jalview.viewmodel.AlignmentViewport;
 
 import java.util.List;
 
@@ -23,7 +23,7 @@ public class ScaleRendererTest
     String data = ">Seq/20-45\nABCDEFGHIJKLMNOPQRSTUVWXYS\n";
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(data,
             DataSourceType.PASTE);
-    AlignViewport av = af.getViewport();
+    AlignmentViewport av = af.getViewport();
 
     /*
      * scale has minor ticks at 5, 15, 25, major at 10 and 20

diff --git a/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java b/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
index d8b905e..76e4fc5 100644 (file)
--- a/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
+++ b/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
@@ -6,11 +6,11 @@ import static org.testng.Assert.assertNotEquals;
 import static org.testng.Assert.assertNull;
 import static org.testng.Assert.assertTrue;
 
+import jalview.api.AlignViewportI;
 import jalview.api.FeatureColourI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
-import jalview.gui.AlignViewport;
 import jalview.gui.FeatureRenderer;
 import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
@@ -43,7 +43,7 @@ import org.testng.annotations.Test;
  */
 public class FeatureColourFinderTest
 {
-  private AlignViewport av;
+  private AlignViewportI av;
 
   private SequenceI seq;
 

diff --git a/test/jalview/schemes/PIDColourSchemeTest.java b/test/jalview/schemes/PIDColourSchemeTest.java
index fa4b5d9..c2f86d6 100644 (file)
--- a/test/jalview/schemes/PIDColourSchemeTest.java
+++ b/test/jalview/schemes/PIDColourSchemeTest.java
@@ -4,9 +4,9 @@ import static org.testng.Assert.assertEquals;
 
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
-import jalview.gui.AlignViewport;
 import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
+import jalview.viewmodel.AlignmentViewport;
 
 import java.awt.Color;
 
@@ -83,7 +83,7 @@ public class PIDColourSchemeTest
      */
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqs,
             DataSourceType.PASTE);
-    AlignViewport viewport = af.getViewport();
+    AlignmentViewport viewport = af.getViewport();
     viewport.setIgnoreGapsConsensus(false, af.alignPanel);
     while (viewport.getConsensusSeq() == null)
     {