JAL-1896 revised implementation to construct a ColourSchemeI instance after creating...

diff --git a/src/jalview/api/ComplexAlignFile.java b/src/jalview/api/ComplexAlignFile.java
index 4ac08cf..2bf2782 100644 (file)
--- a/src/jalview/api/ComplexAlignFile.java
+++ b/src/jalview/api/ComplexAlignFile.java
@@ -22,7 +22,6 @@ package jalview.api;
 
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SequenceI;
-import jalview.schemes.ColourSchemeI;
 
 /**
  * This interface should be implemented by complex file parser with the ability
@@ -44,7 +43,7 @@ public interface ComplexAlignFile
    * 
    * @return
    */
-  public ColourSchemeI getColourScheme();
+  public String getGlobalColourScheme();
 
   /**
    * Retrieves the Column selection/hidden column from a complex file parser

diff --git a/src/jalview/appletgui/CutAndPasteTransfer.java b/src/jalview/appletgui/CutAndPasteTransfer.java
index 4590c54..1ee8393 100644 (file)
--- a/src/jalview/appletgui/CutAndPasteTransfer.java
+++ b/src/jalview/appletgui/CutAndPasteTransfer.java
@@ -33,6 +33,7 @@ import jalview.io.FileParse;
 import jalview.io.IdentifyFile;
 import jalview.io.NewickFile;
 import jalview.io.TCoffeeScoreFile;
+import jalview.json.binding.biojson.v1.ColourSchemeMapper;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.TCoffeeColourScheme;
 import jalview.util.MessageManager;
@@ -259,11 +260,14 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
                   .getHiddenSequences();
           boolean showSeqFeatures = ((ComplexAlignFile) source)
                   .isShowSeqFeatures();
-          ColourSchemeI cs = ((ComplexAlignFile) source).getColourScheme();
+          String colourSchemeName = ((ComplexAlignFile) source)
+                  .getGlobalColourScheme();
           af = new AlignFrame(al, hiddenSeqs, colSel,
                   alignFrame.viewport.applet, "Cut & Paste input - "
                           + format, false);
           af.getAlignViewport().setShowSequenceFeatures(showSeqFeatures);
+          ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
+                  colourSchemeName, al);
           af.changeColour(cs);
         }
         else

diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index f5a8e1c..acc71f3 100644 (file)
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -35,6 +35,7 @@ import jalview.io.IdentifyFile;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
 import jalview.jbgui.GCutAndPasteTransfer;
+import jalview.json.binding.biojson.v1.ColourSchemeMapper;
 import jalview.schemes.ColourSchemeI;
 import jalview.util.MessageManager;
 
@@ -262,13 +263,16 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
                   .getHiddenSequences();
           boolean showSeqFeatures = ((ComplexAlignFile) source)
                   .isShowSeqFeatures();
-          ColourSchemeI cs = ((ComplexAlignFile) source).getColourScheme();
+          String colourSchemeName = ((ComplexAlignFile) source)
+                  .getGlobalColourScheme();
           FeaturesDisplayedI fd = ((ComplexAlignFile) source)
                   .getDisplayedFeatures();
           af = new AlignFrame(al, hiddenSeqs, colSel,
                   AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
           af.getViewport().setShowSequenceFeatures(showSeqFeatures);
           af.getViewport().setFeaturesDisplayed(fd);
+          ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
+                  colourSchemeName, al);
           af.changeColour(cs);
         }
         else

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 9ff3ef9..9931f32 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -31,6 +31,7 @@ import jalview.gui.AlignFrame;
 import jalview.gui.AlignViewport;
 import jalview.gui.Desktop;
 import jalview.gui.Jalview2XML;
+import jalview.json.binding.biojson.v1.ColourSchemeMapper;
 import jalview.schemes.ColourSchemeI;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
@@ -375,8 +376,8 @@ public class FileLoader implements Runnable
                       .getHiddenSequences();
               boolean showSeqFeatures = ((ComplexAlignFile) source)
                       .isShowSeqFeatures();
-              ColourSchemeI cs = ((ComplexAlignFile) source)
-                      .getColourScheme();
+              String colourSchemeName = ((ComplexAlignFile) source)
+                      .getGlobalColourScheme();
               FeaturesDisplayedI fd = ((ComplexAlignFile) source)
                       .getDisplayedFeatures();
               alignFrame = new AlignFrame(al, hiddenSeqs, colSel,
@@ -385,6 +386,8 @@ public class FileLoader implements Runnable
               alignFrame.getViewport().setShowSequenceFeatures(
                       showSeqFeatures);
               alignFrame.getViewport().setFeaturesDisplayed(fd);
+              ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
+                      colourSchemeName, al);
               alignFrame.changeColour(cs);
             }
             else

diff --git a/src/jalview/io/HtmlFile.java b/src/jalview/io/HtmlFile.java
index 06c2717..954d12e 100644 (file)
--- a/src/jalview/io/HtmlFile.java
+++ b/src/jalview/io/HtmlFile.java
@@ -25,7 +25,6 @@ import jalview.api.ComplexAlignFile;
 import jalview.api.FeaturesDisplayedI;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SequenceI;
-import jalview.schemes.ColourSchemeI;
 
 import java.io.IOException;
 import java.io.StringReader;
@@ -40,7 +39,7 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
 
   public static final String FILE_DESC = "HTML";
 
-  private ColourSchemeI colourScheme;
+  private String globalColourScheme;
 
   private boolean showSeqFeatures;
 
@@ -108,7 +107,7 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
       this.seqGroups = jsonFile.getSeqGroups();
       this.annotations = jsonFile.getAnnotations();
       this.showSeqFeatures = jsonFile.isShowSeqFeatures();
-      this.colourScheme = jsonFile.getColourScheme();
+      this.globalColourScheme = jsonFile.getGlobalColourScheme();
       this.hiddenSequences = jsonFile.getHiddenSequences();
       this.columnSelection = jsonFile.getColumnSelection();
       this.displayedFeatures = jsonFile.getDisplayedFeatures();
@@ -135,14 +134,14 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
     this.showSeqFeatures = showSeqFeatures;
   }
 
-  public ColourSchemeI getColourScheme()
+  public String getGlobalColourScheme()
   {
-    return colourScheme;
+    return globalColourScheme;
   }
 
-  public void setColourScheme(ColourSchemeI colourScheme)
+  public void setColourScheme(String globalColourScheme)
   {
-    this.colourScheme = colourScheme;
+    this.globalColourScheme = globalColourScheme;
   }
 
   public ColumnSelection getColumnSelection()

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index 717ab8b..8725556 100644 (file)
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -28,7 +28,6 @@ import jalview.api.ComplexAlignFile;
 import jalview.api.FeatureRenderer;
 import jalview.api.FeaturesDisplayedI;
 import jalview.bin.BuildDetails;
-import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
@@ -45,7 +44,6 @@ import jalview.json.binding.biojson.v1.ColourSchemeMapper;
 import jalview.json.binding.biojson.v1.SequenceFeaturesPojo;
 import jalview.json.binding.biojson.v1.SequenceGrpPojo;
 import jalview.json.binding.biojson.v1.SequencePojo;
-import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
 
@@ -64,8 +62,6 @@ import org.json.simple.parser.JSONParser;
 
 public class JSONFile extends AlignFile implements ComplexAlignFile
 {
-  private ColourSchemeI colourScheme;
-
   private static String version = new BuildDetails().getVersion();
 
   private String webstartUrl = "http://www.jalview.org/services/launchApp";
@@ -76,7 +72,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
 
   public static final String FILE_DESC = "JSON";
 
-  private String globalColorScheme;
+  private String globalColourScheme;
 
   private boolean showSeqFeatures;
 
@@ -184,7 +180,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
         jsonSeqPojo.setSeq(seq.getSequenceAsString());
         jsonAlignmentPojo.getSeqs().add(jsonSeqPojo);
       }
-      jsonAlignmentPojo.setGlobalColorScheme(globalColorScheme);
+      jsonAlignmentPojo.setGlobalColorScheme(globalColourScheme);
       jsonAlignmentPojo.getAppSettings().put("application", application);
       jsonAlignmentPojo.getAppSettings().put("version", version);
       jsonAlignmentPojo.getAppSettings().put("webStartUrl", webstartUrl);
@@ -389,7 +385,6 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
   @SuppressWarnings("unchecked")
   public JSONFile parse(Reader jsonAlignmentString)
   {
-    String jsColourScheme = null;
     try
     {
       JSONParser jsonParser = new JSONParser();
@@ -407,7 +402,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
 
       if (jvSettingsJsonObj != null)
       {
-        jsColourScheme = (String) jvSettingsJsonObj
+        globalColourScheme = (String) jvSettingsJsonObj
                 .get("globalColorScheme");
         Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
                 "showSeqFeatures").toString());
@@ -437,12 +432,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
         seqMap.put(seqUniqueId, seq);
       }
 
-      if (jsColourScheme != null)
-      {
-        setColourScheme(ColourSchemeMapper.getJalviewColourScheme(
-                jsColourScheme,
-                new Alignment(seqs.toArray(new SequenceI[0]))));
-      }
+
       parseFeatures(jsonSeqArray);
 
       for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
@@ -529,7 +519,6 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
                 .toString(), annotations);
         this.annotations.add(alignAnnot);
       }
-
     } catch (Exception e)
     {
       e.printStackTrace();
@@ -609,24 +598,14 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     }
   }
 
-  public String getGlobalColorScheme()
-  {
-    return globalColorScheme;
-  }
-
-  public void setGlobalColorScheme(String globalColorScheme)
-  {
-    this.globalColorScheme = globalColorScheme;
-  }
-
-  public ColourSchemeI getColourScheme()
+  public String getGlobalColourScheme()
   {
-    return colourScheme;
+    return globalColourScheme;
   }
 
-  public void setColourScheme(ColourSchemeI colourScheme)
+  public void setGlobalColorScheme(String globalColourScheme)
   {
-    this.colourScheme = colourScheme;
+    this.globalColourScheme = globalColourScheme;
   }
 
   @Override
@@ -662,7 +641,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
         annotations.add(annot);
       }
     }
-    globalColorScheme = ColourSchemeProperty.getColourName(viewport
+    globalColourScheme = ColourSchemeProperty.getColourName(viewport
             .getGlobalColourScheme());
     setDisplayedFeatures(viewport.getFeaturesDisplayed());
     showSeqFeatures = viewport.isShowSequenceFeatures();

diff --git a/src/jalview/json/binding/biojson/v1/ColourSchemeMapper.java b/src/jalview/json/binding/biojson/v1/ColourSchemeMapper.java
index de4ba8d..aeab34c 100644 (file)
--- a/src/jalview/json/binding/biojson/v1/ColourSchemeMapper.java
+++ b/src/jalview/json/binding/biojson/v1/ColourSchemeMapper.java
@@ -40,42 +40,60 @@ import jalview.schemes.ZappoColourScheme;
 
 public class ColourSchemeMapper
 {
+  private static ColourSchemeI csZappo, csTaylor, csNucleotide, csPurine,
+          csHelix, csTurn, csStrand, csBuried, csHydro,
+          csRNAInteractionType, csPID, csBlosum62 = null;
+  static
+  {
+    csZappo = new ZappoColourScheme();
+    csTaylor = new TaylorColourScheme();
+    csNucleotide = new NucleotideColourScheme();
+    csPurine = new PurinePyrimidineColourScheme();
+    csHelix = new HelixColourScheme();
+    csTurn = new TurnColourScheme();
+    csStrand = new StrandColourScheme();
+    csBuried = new BuriedColourScheme();
+    csHydro = new HydrophobicColourScheme();
+    csRNAInteractionType = new RNAInteractionColourScheme();
+    csPID = new PIDColourScheme();
+    csBlosum62 = new Blosum62ColourScheme();
+  }
   public static ColourSchemeI getJalviewColourScheme(
           String colourSchemeName, AnnotatedCollectionI annotCol)
   {
     switch (colourSchemeName.toUpperCase())
     {
     case "ZAPPO":
-      return new ZappoColourScheme();
+      return csZappo;
     case "TAYLOR":
-      return new TaylorColourScheme();
+      return csTaylor;
     case "NUCLEOTIDE":
-      return new NucleotideColourScheme();
+      return csNucleotide;
     case "PURINE":
     case "PURINE/PYRIMIDINE":
-      return new PurinePyrimidineColourScheme();
+      return csPurine;
     case "HELIX":
     case "HELIX PROPENSITY":
-      return new HelixColourScheme();
+      return csHelix;
     case "TURN":
     case "TURN PROPENSITY":
-      return new TurnColourScheme();
+      return csTurn;
     case "STRAND":
     case "STRAND PROPENSITY":
-      return new StrandColourScheme();
+      return csStrand;
     case "BURIED":
     case "BURIED INDEX":
-      return new BuriedColourScheme();
+      return csBuried;
     case "HYDRO":
     case "HYDROPHOBIC":
-      return new HydrophobicColourScheme();
+      return csHydro;
     case "RNA INTERACTION TYPE":
-      return new RNAInteractionColourScheme();
+      return csRNAInteractionType;
     case "PID":
     case "% IDENTITY":
-      return new PIDColourScheme();
+      return csPID;
     case "BLOSUM62":
-      return new Blosum62ColourScheme();
+      return csBlosum62;
     case "T-COFFEE SCORES":
       return (annotCol != null) ? new TCoffeeColourScheme(annotCol) : null;
     case "RNA HELICES":

diff --git a/test/jalview/io/JSONFileTest.java b/test/jalview/io/JSONFileTest.java
index 4371ff9..4c2757f 100644 (file)
--- a/test/jalview/io/JSONFileTest.java
+++ b/test/jalview/io/JSONFileTest.java
@@ -35,7 +35,6 @@ import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
 import jalview.json.binding.biojson.v1.ColourSchemeMapper;
 import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ZappoColourScheme;
 
 import java.io.IOException;
 import java.util.ArrayList;
@@ -235,7 +234,10 @@ public class JSONFileTest
               jf.getColumnSelection(), AlignFrame.DEFAULT_WIDTH,
               AlignFrame.DEFAULT_HEIGHT);
       af.getViewport().setShowSequenceFeatures(jf.isShowSeqFeatures());
-      af.changeColour(jf.getColourScheme());
+      String colourSchemeName = jf.getGlobalColourScheme();
+      ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
+              colourSchemeName, alignment);
+      af.changeColour(cs);
       af.getViewport().setFeaturesDisplayed(jf.getDisplayedFeatures());
 
       formatAdapter = new AppletFormatAdapter(af.alignPanel, exportSettings);
@@ -318,11 +320,13 @@ public class JSONFileTest
   @Test(groups = { "Functional" })
   public void colorSchemeTest()
   {
-    Assert.assertNotNull(testJsonFile.getColourScheme(),
+    Assert.assertNotNull(testJsonFile.getGlobalColourScheme(),
             "Colourscheme is null, parsing failed!");
-    Assert.assertTrue(
-            testJsonFile.getColourScheme() instanceof ZappoColourScheme,
+    Assert.assertEquals(testJsonFile.getGlobalColourScheme(), "Zappo",
             "Zappo colour scheme expected!");
+    // Assert.assertTrue(
+    // testJsonFile.getGlobalColourScheme() instanceof ZappoColourScheme,
+    // "Zappo colour scheme expected!");
   }
 
   @Test(groups = { "Functional" })