JAL-3895 alphafold colours via pluggable annotation row builder. Also ensures min...

diff --git a/src/jalview/datamodel/annotations/AlphaFoldAnnotationRowBuilder.java b/src/jalview/datamodel/annotations/AlphaFoldAnnotationRowBuilder.java
new file mode 100644 (file)
index 0000000..60e6866
--- /dev/null
+++ b/src/jalview/datamodel/annotations/AlphaFoldAnnotationRowBuilder.java
@@ -0,0 +1,38 @@
+package jalview.datamodel.annotations.AnnotationRowBuilder;
+
+import jalview.datamodel.Annotation;
+
+public class AlphaFoldAnnotationRowBuilder extends AnnotationRowBuilder
+{
+  public AlphaFoldAnnotationRowBuilder()
+  {
+    super("Alphafold Reliability");
+    min = 0;
+    max = 100;
+    hasMinMax = true;
+  }
+
+  @Override
+  public void processAnnotation(Annotation annotation)
+  {
+    if (annotation.value > 90)
+    {
+      // Very High
+      annotation.colour = new java.awt.Color(0, 83, 214);
+    }
+    if (annotation.value <= 90)
+    {
+      // High
+      annotation.colour = new java.awt.Color(101, 203, 243);
+    }
+    if (annotation.value <= 70)
+    {
+      // Confident
+      annotation.colour = new java.awt.Color(255, 219, 19);
+    }
+    if (annotation.value < 50)
+    {
+      annotation.colour = new java.awt.Color(255, 125, 69);
+    }
+  }
+}
\ No newline at end of file

diff --git a/src/jalview/datamodel/annotations/AnnotationRowBuilder.java b/src/jalview/datamodel/annotations/AnnotationRowBuilder.java
new file mode 100644 (file)
index 0000000..b802612
--- /dev/null
+++ b/src/jalview/datamodel/annotations/AnnotationRowBuilder.java
@@ -0,0 +1,101 @@
+package jalview.datamodel.annotations.AnnotationRowBuilder;
+
+import jalview.datamodel.Annotation;
+
+public class AnnotationRowBuilder
+{
+
+  String name;
+
+  boolean hasDescription = false;
+
+  String description;
+
+  boolean hasMinMax = false;
+
+  public String getName()
+  {
+    return name;
+  }
+
+  public void setName(String name)
+  {
+    this.name = name;
+  }
+
+  public boolean isHasDescription()
+  {
+    return hasDescription;
+  }
+
+  public void setHasDescription(boolean hasDescription)
+  {
+    this.hasDescription = hasDescription;
+  }
+
+  public String getDescription()
+  {
+    return description;
+  }
+
+  public void setDescription(String description)
+  {
+    this.description = description;
+  }
+
+  public boolean isHasMinMax()
+  {
+    return hasMinMax;
+  }
+
+  public void setHasMinMax(boolean hasMinMax)
+  {
+    this.hasMinMax = hasMinMax;
+  }
+
+  public float getMin()
+  {
+    return min;
+  }
+
+  public void setMin(float min)
+  {
+    this.min = min;
+  }
+
+  public float getMax()
+  {
+    return max;
+  }
+
+  public void setMax(float max)
+  {
+    this.max = max;
+  }
+
+  float min, max;
+
+  public AnnotationRowBuilder(String string)
+  {
+    name = string;
+  }
+
+  public AnnotationRowBuilder(String name, float min, float max)
+  {
+    this(name);
+    this.min = min;
+    this.max = max;
+    this.hasMinMax = true;
+  }
+
+  /**
+   * override this to apply some form of transformation to the annotation - eg a
+   * colourscheme
+   * 
+   * @param annotation
+   */
+  public void processAnnotation(Annotation annotation)
+  {
+
+  }
+}

diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java
index ab6bbcc..05c3f7a 100644 (file)
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -20,23 +20,11 @@
  */
 package jalview.ext.jmol;
 
-import java.util.Locale;
-
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.io.DataSourceType;
-import jalview.io.FileParse;
-import jalview.io.StructureFile;
-import jalview.schemes.ResidueProperties;
-import jalview.util.Format;
-import jalview.util.MessageManager;
-
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 import java.util.Vector;
 
@@ -49,6 +37,18 @@ import org.jmol.viewer.Viewer;
 
 import com.stevesoft.pat.Regex;
 
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.annotations.AnnotationRowBuilder.AlphaFoldAnnotationRowBuilder;
+import jalview.datamodel.annotations.AnnotationRowBuilder.AnnotationRowBuilder;
+import jalview.io.DataSourceType;
+import jalview.io.FileParse;
+import jalview.io.StructureFile;
+import jalview.schemes.ResidueProperties;
+import jalview.util.Format;
+import jalview.util.MessageManager;
 import mc_view.Atom;
 import mc_view.PDBChain;
 import mc_view.Residue;
@@ -238,13 +238,14 @@ public class JmolParser extends StructureFile implements JmolStatusListener
         }
         else
         {
+          AnnotationRowBuilder builder = null;
           String tempFString = null;
           if (isAlphafoldModel())
           {
-            tempFString = "Alphafold Reliability";
+            builder = new AlphaFoldAnnotationRowBuilder();
           }
 
-          tmpchain = new PDBChain(getId(), tmpatom.chain, tempFString);
+          tmpchain = new PDBChain(getId(), tmpatom.chain, builder);
           getChains().add(tmpchain);
           tmpchain.atoms.addElement(tmpatom);
         }

diff --git a/src/mc_view/PDBChain.java b/src/mc_view/PDBChain.java
index 72d276e..d9e7ec9 100755 (executable)
--- a/src/mc_view/PDBChain.java
+++ b/src/mc_view/PDBChain.java
@@ -20,6 +20,11 @@
  */
 package mc_view;
 
+import java.awt.Color;
+import java.util.List;
+import java.util.Locale;
+import java.util.Vector;
+
 import jalview.analysis.AlignSeq;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
@@ -27,17 +32,13 @@ import jalview.datamodel.Mapping;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.annotations.AnnotationRowBuilder.AnnotationRowBuilder;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ResidueProperties;
 import jalview.structure.StructureImportSettings;
 import jalview.structure.StructureMapping;
 import jalview.util.Comparison;
 
-import java.awt.Color;
-import java.util.List;
-import java.util.Locale;
-import java.util.Vector;
-
 public class PDBChain
 {
   public static final String RESNUM_FEATURE = "RESNUM";
@@ -79,17 +80,16 @@ public class PDBChain
 
   public String pdbid = "";
 
-  String tfacName = "Temperature Factor";
+  AnnotationRowBuilder tfacTemplate = new AnnotationRowBuilder(
+          "TemperatureFactor");
 
   public PDBChain(String thePdbid, String theId,
-          String tempFactorColumnName)
+          AnnotationRowBuilder template)
   {
-    this.pdbid = thePdbid == null ? thePdbid
-            : thePdbid.toLowerCase(Locale.ROOT);
-    this.id = theId;
-    if (tempFactorColumnName != null && tempFactorColumnName.length() > 0)
+    this(thePdbid, theId);
+    if (template != null)
     {
-      tfacName = tempFactorColumnName;
+      tfacTemplate = template;
     }
   }
 
@@ -102,7 +102,9 @@ public class PDBChain
    */
   public PDBChain(String thePdbid, String theId)
   {
-    this(thePdbid, theId, null);
+    this.pdbid = thePdbid == null ? thePdbid
+            : thePdbid.toLowerCase(Locale.ROOT);
+    this.id = theId;
   }
 
   /**
@@ -516,14 +518,23 @@ public class PDBChain
       for (int i = 0; i < iSize; i++)
       {
         annots[i] = resAnnotation.elementAt(i);
+        tfacTemplate.processAnnotation(annots[i]);
         max = Math.max(max, annots[i].value);
         min = Math.min(min, annots[i].value);
         resAnnotation.setElementAt(null, i);
       }
-      AlignmentAnnotation tfactorann = new AlignmentAnnotation(tfacName,
-              tfacName + " for " + pdbid + id, annots, min, max,
-              AlignmentAnnotation.LINE_GRAPH);
+      if (tfacTemplate.isHasMinMax())
+      {
+        max = tfacTemplate.getMax();
+        min = tfacTemplate.getMin();
+      }
 
+      AlignmentAnnotation tfactorann = new AlignmentAnnotation(
+              tfacTemplate.getName(),
+              (tfacTemplate.isHasDescription()
+                      ? tfacTemplate.getDescription()
+                      : tfacTemplate.getName()) + " for " + pdbid + id,
+              annots, min, max, AlignmentAnnotation.LINE_GRAPH);
       tfactorann.setCalcId(getClass().getName());
 
       tfactorann.setSequenceRef(sequence);
@@ -694,8 +705,8 @@ public class PDBChain
         // Useful for debugging mappings - adds annotation for mapped position
         float min = -1, max = 0;
         Annotation[] an = new Annotation[sq.getEnd() - sq.getStart() + 1];
-        for (int i = sq.getStart(), j = sq
-                .getEnd(), k = 0; i <= j; i++, k++)
+        for (int i = sq.getStart(), j = sq.getEnd(),
+                k = 0; i <= j; i++, k++)
         {
           int prn = mapping.getPDBResNum(k + 1);