Merge branch 'develop' into Release_2_9_0b1_Branch

[jalview.git] / src / jalview / io / JSONFile.java

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index 6fe06eb..8e87953 100644 (file)
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -39,12 +39,14 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.json.binding.biojson.v1.AlignmentAnnotationPojo;
 import jalview.json.binding.biojson.v1.AlignmentPojo;
+import jalview.json.binding.biojson.v1.AnnotationDisplaySettingPojo;
 import jalview.json.binding.biojson.v1.AnnotationPojo;
 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.ColourSchemeProperty;
+import jalview.schemes.UserColourScheme;
 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
 
 import java.awt.Color;
@@ -90,6 +92,8 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
 
   private ArrayList<SequenceI> hiddenSequences;
 
+  private final static String TCOFFEE_SCORE = "TCoffeeScore";
+
   public JSONFile()
   {
     super();
@@ -211,7 +215,10 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
       }
       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");
         }
@@ -367,6 +374,26 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
       AlignmentAnnotationPojo alignAnnotPojo = new AlignmentAnnotationPojo();
       alignAnnotPojo.setDescription(annot.description);
       alignAnnotPojo.setLabel(annot.label);
+      if (!Double.isNaN(annot.score))
+      {
+        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.scaleColLabel);
+      annotSetting.setShowAllColLabels(annot.showAllColLabels);
+      annotSetting.setVisible(annot.visible);
+      annotSetting.setHasIcon(annot.hasIcons);
+      alignAnnotPojo.setAnnotationSettings(annotSetting);
+      SequenceI refSeq = annot.sequenceRef;
+      if (refSeq != null)
+      {
+        alignAnnotPojo.setSequenceRef(String.valueOf(refSeq.hashCode()));
+      }
       for (Annotation annotation : annot.annotations)
       {
         AnnotationPojo annotationPojo = new AnnotationPojo();
@@ -376,12 +403,28 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
           annotationPojo.setValue(annotation.value);
           annotationPojo
                   .setSecondaryStructure(annotation.secondaryStructure);
-          annotationPojo.setDisplayCharacter(annotation.displayCharacter);
+          String displayChar = annotation.displayCharacter == null ? null
+                  : annotation.displayCharacter;
+          // System.out.println("--------------------->[" + displayChar + "]");
+          annotationPojo.setDisplayCharacter(displayChar);
+          if (annotation.colour != null)
+          {
+            annotationPojo.setColour(jalview.util.Format
+                    .getHexString(annotation.colour));
+          }
           alignAnnotPojo.getAnnotations().add(annotationPojo);
         }
         else
         {
-          alignAnnotPojo.getAnnotations().add(annotationPojo);
+          if (annot.getCalcId() != null
+                  && annot.getCalcId().equalsIgnoreCase(TCOFFEE_SCORE))
+          {
+            // do nothing
+          }
+          else
+          {
+            alignAnnotPojo.getAnnotations().add(annotationPojo);
+          }
         }
       }
       jsonAnnotations.add(alignAnnotPojo);
@@ -439,7 +482,6 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
         seqMap.put(seqUniqueId, seq);
       }
 
-
       parseFeatures(jsonSeqArray);
 
       for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
@@ -478,8 +520,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
           }
         }
         SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
-                displayBoxes, displayText, colourText,
-                startRes, endRes);
+                displayBoxes, displayText, colourText, startRes, endRes);
         seqGrp.cs = ColourSchemeMapper.getJalviewColourScheme(colourScheme,
                 seqGrp);
         seqGrp.setShowNonconserved(showNonconserved);
@@ -517,6 +558,12 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
                     : annot.get("displayCharacter").toString();
 
             annotations[count] = new Annotation(displayChar, desc, ss, val);
+            if (annot.get("colour") != null)
+            {
+              Color color = UserColourScheme.getColourFromString(annot.get(
+                      "colour").toString());
+              annotations[count].colour = color;
+            }
           }
           ++count;
         }
@@ -524,7 +571,64 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
         AlignmentAnnotation alignAnnot = new AlignmentAnnotation(alAnnot
                 .get("label").toString(), alAnnot.get("description")
                 .toString(), annotations);
+        alignAnnot.graph = (alAnnot.get("graphType") == null) ? 0 : Integer
+                .valueOf(alAnnot.get("graphType").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.hasIcons = (diplaySettings.get("hasIcon") == null) ? true
+                  : Boolean.valueOf(diplaySettings.get("hasIcon")
+                          .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;
+
+        Sequence sequence = (seqHash != null) ? seqMap.get(seqHash) : null;
+        if (sequence != null)
+        {
+          alignAnnot.sequenceRef = sequence;
+          sequence.addAlignmentAnnotation(alignAnnot);
+          if (alignAnnot.label.equalsIgnoreCase("T-COFFEE"))
+          {
+            alignAnnot.createSequenceMapping(sequence, sequence.getStart(),
+                    false);
+            sequence.addAlignmentAnnotation(alignAnnot);
+            alignAnnot.adjustForAlignment();
+          }
+        }
+        alignAnnot.validateRangeAndDisplay();
         this.annotations.add(alignAnnot);
+
       }
     } catch (Exception e)
     {
@@ -641,10 +745,6 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     {
       if (annot != null && !annot.autoCalculated)
       {
-        if (!annot.visible)
-        {
-          continue;
-        }
         annotations.add(annot);
       }
     }