From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Thu, 1 Oct 2015 13:50:52 +0000 (+0100)
Subject: JAL-1912 refactor annotation refsequence assignemnt mechanism
X-Git-Tag: Release_2_10_0~365^2~8
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=384e43c561fbc2446923dd2ed227e2931a8ac406;p=jalview.git

JAL-1912 refactor annotation refsequence assignemnt mechanism
---

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index 3a08409..4e293db 100644
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -211,12 +211,14 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
       if (exportSettings.isExportAnnotations())
       {
         jsonAlignmentPojo
-.setAlignAnnotation(annotationToJsonPojo(
-                annotations, seqs));
+                .setAlignAnnotation(annotationToJsonPojo(annotations));
       }
       else
       {
-        if (globalColourScheme.equalsIgnoreCase("RNA Helices"))
+        // These color schemes require annotation, disable them if annotations
+        // are not exported
+        if (globalColourScheme.equalsIgnoreCase("RNA Helices")
+                || globalColourScheme.equalsIgnoreCase("T-COFFEE SCORES"))
         {
           jsonAlignmentPojo.setGlobalColorScheme("None");
         }
@@ -360,7 +362,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
   }
 
   public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
-          Vector<AlignmentAnnotation> annotations, Vector<SequenceI> seqs)
+          Vector<AlignmentAnnotation> annotations)
   {
     List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<AlignmentAnnotationPojo>();
     if (annotations == null)
@@ -369,24 +371,25 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     }
     for (AlignmentAnnotation annot : annotations)
     {
+      AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
+      alignAnnotPojo.setDescription(annot.description);
+      alignAnnotPojo.setLabel(annot.label);
+      alignAnnotPojo.setScore(annot.score);
+      alignAnnotPojo.setCalcId(annot.getCalcId());
+      alignAnnotPojo.setGraphType(annot.graph);
+
       AnnotationDisplaySettingPojo annotSetting = new AnnotationDisplaySettingPojo();
       annotSetting.setBelowAlignment(annot.belowAlignment);
       annotSetting.setCentreColLabels(annot.centreColLabels);
       annotSetting.setScaleColLabel(annot.centreColLabels);
       annotSetting.setShowAllColLabels(annot.showAllColLabels);
       annotSetting.setVisible(annot.visible);
-
-
-      AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
-      alignAnnotPojo.setScore(annot.score);
-      alignAnnotPojo.setCalcId(annot.getCalcId());
-      alignAnnotPojo.setDescription(annot.description);
-      alignAnnotPojo.setLabel(annot.label);
-      alignAnnotPojo.setGraphType(annot.graph);
       alignAnnotPojo.setAnnotationSettings(annotSetting);
-      int seqHash = setAnnotationRefSeq(annot, seqs);
-      alignAnnotPojo.setSequenceRef(seqHash == 0 ? null : String
-              .valueOf(seqHash));
+      SequenceI refSeq = annot.sequenceRef;
+      if (refSeq != null)
+      {
+        alignAnnotPojo.setSequenceRef(String.valueOf(refSeq.hashCode()));
+      }
       for (Annotation annotation : annot.annotations)
       {
         AnnotationPojo annotationPojo = new AnnotationPojo();
@@ -413,7 +416,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
           }
           else
           {
-            alignAnnotPojo.getAnnotations().add(null);
+            alignAnnotPojo.getAnnotations().add(annotationPojo);
           }
         }
       }
@@ -422,29 +425,6 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     return jsonAnnotations;
   }
 
-  private static int setAnnotationRefSeq(AlignmentAnnotation annot,
-          Vector<SequenceI> seqs)
-  {
-    if (annot == null || seqs == null || seqs.size() == 0)
-    {
-      return 0;
-    }
-    for (SequenceI seq : seqs)
-    {
-      if (seq == null || seq.getAnnotation() == null)
-      {
-        continue;
-      }
-      for (AlignmentAnnotation seqAnnot : seq.getAnnotation())
-      {
-        if (seqAnnot == annot)
-        {
-          return seq.hashCode();
-        }
-      }
-    }
-    return 0;
-  }
   @SuppressWarnings("unchecked")
   public JSONFile parse(Reader jsonAlignmentString)
   {
@@ -552,14 +532,10 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
         {
           continue;
         }
-        JSONObject diplaySettings = (JSONObject) alAnnot
-                .get("annotationSettings");
 
         JSONArray annotJsonArray = (JSONArray) alAnnot.get("annotations");
         Annotation[] annotations = new Annotation[annotJsonArray.size()];
         int count = 0;
-        String calcId = alAnnot.get("calcId") == null ? "" : alAnnot.get(
-                "calcId").toString();
         for (Iterator<JSONObject> annotIter = annotJsonArray.iterator(); annotIter
                 .hasNext();)
         {
@@ -595,24 +571,39 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
         alignAnnot.graph = (alAnnot.get("graphType") == null) ? 0 : Integer
                 .valueOf(alAnnot.get("graphType")
                         .toString());
-        alignAnnot.scaleColLabel = (diplaySettings.get("scaleColLabel") == null) ? false
-                : Boolean.valueOf(diplaySettings.get("scaleColLabel")
-                        .toString());
-        alignAnnot.showAllColLabels = (diplaySettings
-                .get("showAllColLabels") == null) ? true : Boolean
-                .valueOf(diplaySettings.get("showAllColLabels").toString());
-        alignAnnot.centreColLabels = (diplaySettings.get("centreColLabels") == null) ? true
-                : Boolean.valueOf(diplaySettings.get("centreColLabels")
-                        .toString());
-        alignAnnot.belowAlignment = (diplaySettings.get("belowAlignment") == null) ? false
-                : Boolean.valueOf(diplaySettings.get("belowAlignment")
-                        .toString());
-        alignAnnot.visible = (diplaySettings.get("visible") == null) ? true
-                : Boolean.valueOf(diplaySettings.get("visible").toString());
 
+        JSONObject diplaySettings = (JSONObject) alAnnot
+                .get("annotationSettings");
+        if (diplaySettings != null)
+        {
+
+          alignAnnot.scaleColLabel = (diplaySettings.get("scaleColLabel") == null) ? false
+                  : Boolean.valueOf(diplaySettings.get("scaleColLabel")
+                          .toString());
+          alignAnnot.showAllColLabels = (diplaySettings
+                  .get("showAllColLabels") == null) ? true : Boolean
+                  .valueOf(diplaySettings.get("showAllColLabels")
+                          .toString());
+          alignAnnot.centreColLabels = (diplaySettings
+                  .get("centreColLabels") == null) ? true
+                  : Boolean.valueOf(diplaySettings.get("centreColLabels")
+                          .toString());
+          alignAnnot.belowAlignment = (diplaySettings.get("belowAlignment") == null) ? false
+                  : Boolean.valueOf(diplaySettings.get("belowAlignment")
+                          .toString());
+          alignAnnot.visible = (diplaySettings.get("visible") == null) ? true
+                  : Boolean.valueOf(diplaySettings.get("visible")
+                          .toString());
 
-        alignAnnot.score = alAnnot.get("score") == null ? null : Double
-                .valueOf(alAnnot.get("score").toString());
+        }
+        if (alAnnot.get("score") != null)
+        {
+          alignAnnot.score = Double
+                  .valueOf(alAnnot.get("score").toString());
+        }
+
+        String calcId = (alAnnot.get("calcId") == null) ? "" : alAnnot.get(
+                "calcId").toString();
         alignAnnot.setCalcId(calcId);
         String seqHash = (alAnnot.get("sequenceRef") != null) ? alAnnot
                 .get("sequenceRef").toString() : null;
@@ -631,7 +622,6 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
           }
         }
         this.annotations.add(alignAnnot);
-        alignAnnot.validateRangeAndDisplay();
       }
     } catch (Exception e)
     {
diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index e629932..73d34c2 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -3110,9 +3110,4 @@ public class GAlignFrame extends JInternalFrame
   protected void showComplement_actionPerformed(boolean state)
   {
   }
-
-  public JRadioButtonMenuItem getTcoffeColour()
-  {
-    return tcoffeeColour;
-  }
 }
diff --git a/test/jalview/io/JSONFileTest.java b/test/jalview/io/JSONFileTest.java
index 4c2757f..d327134 100644
--- a/test/jalview/io/JSONFileTest.java
+++ b/test/jalview/io/JSONFileTest.java
@@ -324,9 +324,6 @@ public class JSONFileTest
             "Colourscheme is null, parsing failed!");
     Assert.assertEquals(testJsonFile.getGlobalColourScheme(), "Zappo",
             "Zappo colour scheme expected!");
-    // Assert.assertTrue(
-    // testJsonFile.getGlobalColourScheme() instanceof ZappoColourScheme,
-    // "Zappo colour scheme expected!");
   }
 
   @Test(groups = { "Functional" })