JAL-1912 added support of tcoffee annotation and other per sequence annotation for...

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index eda4a1c..d08e1a3 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -3517,6 +3517,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
                 cs, "Background"));
       }
+      if (cs instanceof TCoffeeColourScheme)
+      {
+        tcoffeeColour.setEnabled(true);
+        tcoffeeColour.setSelected(true);
+      }
     }
 
     viewport.setGlobalColourScheme(cs);

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index 3ac4aa7..3a08409 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();
@@ -207,7 +211,8 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
       if (exportSettings.isExportAnnotations())
       {
         jsonAlignmentPojo
-                .setAlignAnnotation(annotationToJsonPojo(annotations));
+.setAlignAnnotation(annotationToJsonPojo(
+                annotations, seqs));
       }
       else
       {
@@ -355,7 +360,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
   }
 
   public static List<AlignmentAnnotationPojo> annotationToJsonPojo(
-          Vector<AlignmentAnnotation> annotations)
+          Vector<AlignmentAnnotation> annotations, Vector<SequenceI> seqs)
   {
     List<AlignmentAnnotationPojo> jsonAnnotations = new ArrayList<AlignmentAnnotationPojo>();
     if (annotations == null)
@@ -364,9 +369,24 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     }
     for (AlignmentAnnotation annot : annotations)
     {
+      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));
       for (Annotation annotation : annot.annotations)
       {
         AnnotationPojo annotationPojo = new AnnotationPojo();
@@ -377,11 +397,24 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
           annotationPojo
                   .setSecondaryStructure(annotation.secondaryStructure);
           annotationPojo.setDisplayCharacter(annotation.displayCharacter);
+          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(null);
+          }
         }
       }
       jsonAnnotations.add(alignAnnotPojo);
@@ -389,6 +422,29 @@ 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)
   {
@@ -492,9 +548,18 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
               .hasNext();)
       {
         JSONObject alAnnot = alAnnotIter.next();
+        if (alAnnot == null)
+        {
+          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();)
         {
@@ -515,8 +580,11 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
                     .get("secondaryStructure").toString().charAt(0);
             String displayChar = annot.get("displayCharacter") == null ? ""
                     : annot.get("displayCharacter").toString();
-
-            annotations[count] = new Annotation(displayChar, desc, ss, val);
+            Color color = annot.get("colour") == null ? Color.white
+                    : UserColourScheme.getColourFromString(annot.get(
+                    "colour").toString());
+            annotations[count] = new Annotation(displayChar, desc, ss, val,
+                    color);
           }
           ++count;
         }
@@ -524,7 +592,46 @@ 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());
+        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());
+        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();
+          }
+        }
         this.annotations.add(alignAnnot);
+        alignAnnot.validateRangeAndDisplay();
       }
     } catch (Exception e)
     {
@@ -641,10 +748,6 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     {
       if (annot != null && !annot.autoCalculated)
       {
-        if (!annot.visible)
-        {
-          continue;
-        }
         annotations.add(annot);
       }
     }

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 73d34c2..e629932 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -3110,4 +3110,9 @@ public class GAlignFrame extends JInternalFrame
   protected void showComplement_actionPerformed(boolean state)
   {
   }
+
+  public JRadioButtonMenuItem getTcoffeColour()
+  {
+    return tcoffeeColour;
+  }
 }

diff --git a/src/jalview/json/binding/biojson/v1/AlignmentAnnotationPojo.java b/src/jalview/json/binding/biojson/v1/AlignmentAnnotationPojo.java
index 5e43f6d..9ac3957 100644 (file)
--- a/src/jalview/json/binding/biojson/v1/AlignmentAnnotationPojo.java
+++ b/src/jalview/json/binding/biojson/v1/AlignmentAnnotationPojo.java
@@ -41,6 +41,27 @@ public class AlignmentAnnotationPojo
   @Attributes(required = false)
   private List<AnnotationPojo> annotations = new ArrayList<AnnotationPojo>();
 
+  @Attributes(
+    required = false,
+    enums = { "0", "1", "2" },
+    description = "Determines the rendered for the annotation<br><ul><li>0 - No graph</li><li>1 - Bar Graph</li><li>2 - Line graph</li></ul>")
+  private int graphType;
+
+  @Attributes(
+    required = false,
+    description = "Reference to the sequence in the alignment<br> if per-sequence annotation")
+  private String sequenceRef;
+
+  @Attributes(
+    required = false,
+    description = "Stores display settings for an annotation")
+  private AnnotationDisplaySettingPojo annotationSettings;
+
+  @Attributes(required = false, description = "Score of the annotation")
+  private double score;
+
+  private String calcId;
+
   public String getLabel()
   {
     return label;
@@ -71,4 +92,55 @@ public class AlignmentAnnotationPojo
     this.annotations = annotations;
   }
 
+  public String getSequenceRef()
+  {
+    return sequenceRef;
+  }
+
+  public void setSequenceRef(String sequenceRef)
+  {
+    this.sequenceRef = sequenceRef;
+  }
+
+  public int getGraphType()
+  {
+    return graphType;
+  }
+
+  public void setGraphType(int graphType)
+  {
+    this.graphType = graphType;
+  }
+
+  public AnnotationDisplaySettingPojo getAnnotationSettings()
+  {
+    return annotationSettings;
+  }
+
+  public void setAnnotationSettings(
+          AnnotationDisplaySettingPojo annotationSettings)
+  {
+    this.annotationSettings = annotationSettings;
+  }
+
+  public double getScore()
+  {
+    return score;
+  }
+
+  public void setScore(double score)
+  {
+    this.score = score;
+  }
+
+  public String getCalcId()
+  {
+    return calcId;
+  }
+
+  public void setCalcId(String calcId)
+  {
+    this.calcId = calcId;
+  }
+
 }

diff --git a/src/jalview/json/binding/biojson/v1/AnnotationDisplaySettingPojo.java b/src/jalview/json/binding/biojson/v1/AnnotationDisplaySettingPojo.java
new file mode 100644 (file)
index 0000000..a3011a0
--- /dev/null
+++ b/src/jalview/json/binding/biojson/v1/AnnotationDisplaySettingPojo.java
@@ -0,0 +1,64 @@
+package jalview.json.binding.biojson.v1;
+
+public class AnnotationDisplaySettingPojo
+{
+  private boolean scaleColLabel;
+
+  private boolean showAllColLabels;
+
+  private boolean centreColLabels;
+
+  private boolean belowAlignment;
+
+  private boolean visible;
+
+  public boolean isScaleColLabel()
+  {
+    return scaleColLabel;
+  }
+
+  public void setScaleColLabel(boolean scaleColLabel)
+  {
+    this.scaleColLabel = scaleColLabel;
+  }
+
+  public boolean isShowAllColLabels()
+  {
+    return showAllColLabels;
+  }
+
+  public void setShowAllColLabels(boolean showAllColLabels)
+  {
+    this.showAllColLabels = showAllColLabels;
+  }
+
+  public boolean isCentreColLabels()
+  {
+    return centreColLabels;
+  }
+
+  public void setCentreColLabels(boolean centreColLabels)
+  {
+    this.centreColLabels = centreColLabels;
+  }
+
+  public boolean isBelowAlignment()
+  {
+    return belowAlignment;
+  }
+
+  public void setBelowAlignment(boolean belowAlignment)
+  {
+    this.belowAlignment = belowAlignment;
+  }
+
+  public boolean isVisible()
+  {
+    return visible;
+  }
+
+  public void setVisible(boolean visible)
+  {
+    this.visible = visible;
+  }
+}

diff --git a/src/jalview/json/binding/biojson/v1/AnnotationPojo.java b/src/jalview/json/binding/biojson/v1/AnnotationPojo.java
index 407ade4..a4d7f17 100644 (file)
--- a/src/jalview/json/binding/biojson/v1/AnnotationPojo.java
+++ b/src/jalview/json/binding/biojson/v1/AnnotationPojo.java
@@ -43,6 +43,9 @@ public class AnnotationPojo
   @Attributes(required = false, description = "Value of the annotation")
   private float value;
 
+  @Attributes(required = false, description = "Colour for position")
+  private String colour;
+
   public String getDisplayCharacter()
   {
     return displayCharacter;
@@ -83,4 +86,14 @@ public class AnnotationPojo
     this.value = value;
   }
 
+  public String getColour()
+  {
+    return colour;
+  }
+
+  public void setColour(String colour)
+  {
+    this.colour = colour;
+  }
+
 }

diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index 92989fb..7aff05a 100755 (executable)
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -99,7 +99,7 @@ public class UserColourScheme extends ResidueColourScheme
     return schemeName;
   }
 
-  public Color getColourFromString(String colour)
+  public static Color getColourFromString(String colour)
   {
     colour = colour.trim();