JAL-4027 JAL-3858 rename CUSTOM_RENDERER to CONTACT_MATRIX annotation.graph type...

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 3f9c2d9..4861dfd 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -306,7 +306,7 @@ public class AlignmentAnnotation
 
   public static final int LINE_GRAPH = 2;
 
-  public static final int CUSTOMRENDERER = 4;
+  public static final int CONTACT_MAP = 4;
 
   public boolean belowAlignment = true;
 

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index db83e76..6ee324f 100644 (file)
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -567,7 +567,7 @@ public class ColumnSelection
     // viewmodel package
     this.clear();
 
-    if (ann_row.graph == AlignmentAnnotation.CUSTOMRENDERER && (filterParams
+    if (ann_row.graph == AlignmentAnnotation.CONTACT_MAP && (filterParams
             .getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD
             || filterParams
                     .getThresholdType() == AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD))

diff --git a/src/jalview/datamodel/ContactMapHolder.java b/src/jalview/datamodel/ContactMapHolder.java
index 2b5c853..f6ccc6a 100644 (file)
--- a/src/jalview/datamodel/ContactMapHolder.java
+++ b/src/jalview/datamodel/ContactMapHolder.java
@@ -40,10 +40,11 @@ public class ContactMapHolder implements ContactMapHolderI
 
     AlignmentAnnotation aa = new AlignmentAnnotation(cm.getAnnotLabel(),
             cm.getAnnotDescr(), new Annotation[0]);
-    aa.graph = AlignmentAnnotation.CUSTOMRENDERER;
+    aa.graph = AlignmentAnnotation.CONTACT_MAP;
     aa.graphMin = cm.getMin();
     aa.graphMax = cm.getMax();
     aa.editable = false;
+    aa.calcId=cm.getType();
 
     contactmaps.put(aa.annotationId, cm);
     // TODO: contact matrices could be intra or inter - more than one refseq

diff --git a/src/jalview/datamodel/ContactMatrix.java b/src/jalview/datamodel/ContactMatrix.java
index 35ec87b..b4f7c07 100644 (file)
--- a/src/jalview/datamodel/ContactMatrix.java
+++ b/src/jalview/datamodel/ContactMatrix.java
@@ -3,7 +3,7 @@ package jalview.datamodel;
 import java.util.ArrayList;
 import java.util.List;
 
-public class ContactMatrix implements ContactMatrixI
+public abstract class ContactMatrix implements ContactMatrixI
 {
   /**
    * are contacts reflexive ?

diff --git a/src/jalview/datamodel/ContactMatrixI.java b/src/jalview/datamodel/ContactMatrixI.java
index 6860e82..d9afc7f 100644 (file)
--- a/src/jalview/datamodel/ContactMatrixI.java
+++ b/src/jalview/datamodel/ContactMatrixI.java
@@ -17,4 +17,10 @@ public interface ContactMatrixI
 
   String getAnnotLabel();
 
+  /**
+   * string indicating how the contactMatrix should be rendered - stored in calcId
+   * @return 
+   */
+  String getType();
+
 }

diff --git a/src/jalview/datamodel/SeqDistanceContactMatrix.java b/src/jalview/datamodel/SeqDistanceContactMatrix.java
index 7dd9778..0773e12 100644 (file)
--- a/src/jalview/datamodel/SeqDistanceContactMatrix.java
+++ b/src/jalview/datamodel/SeqDistanceContactMatrix.java
@@ -8,6 +8,7 @@ package jalview.datamodel;
  */
 public class SeqDistanceContactMatrix implements ContactMatrixI
 {
+  private static final String SEQUENCE_DISTANCE = "SEQUENCE_DISTANCE";
   private int width = 0;
 
   public SeqDistanceContactMatrix(int width)
@@ -99,4 +100,10 @@ public class SeqDistanceContactMatrix implements ContactMatrixI
   {
     return "Sequence Distance";
   }
+
+  @Override
+  public String getType()
+  {
+    return SEQUENCE_DISTANCE;
+  }
 }

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index e146754..a97e0e4 100755 (executable)
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -589,7 +589,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     if (graphStretch != -1)
     {
 
-      if (aa[graphStretch].graph == AlignmentAnnotation.CUSTOMRENDERER)
+      if (aa[graphStretch].graph == AlignmentAnnotation.CONTACT_MAP)
       {
         if (evt.isAltDown() || evt.isAltGraphDown())
         {
@@ -823,7 +823,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
          * but could also be a matrix drag
          */
         if ((evt.isAltDown() || evt.isAltGraphDown()) && (av.getAlignment()
-                .getAlignmentAnnotation()[graphStretch].graph == AlignmentAnnotation.CUSTOMRENDERER))
+                .getAlignmentAnnotation()[graphStretch].graph == AlignmentAnnotation.CONTACT_MAP))
         {
           /*
            * dragging in a matrix
@@ -1146,7 +1146,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       tooltip = ann.annotations[column].description;
     }
     // TODO abstract tooltip generator so different implementations can be built
-    if (ann.graph == AlignmentAnnotation.CUSTOMRENDERER)
+    if (ann.graph == AlignmentAnnotation.CONTACT_MAP)
     {
       ContactListI clist = av.getContactList(ann, column);
       if (clist != null)

diff --git a/src/jalview/io/PContactPredictionFile.java b/src/jalview/io/PContactPredictionFile.java
index 92500c0..de02939 100644 (file)
--- a/src/jalview/io/PContactPredictionFile.java
+++ b/src/jalview/io/PContactPredictionFile.java
@@ -44,6 +44,8 @@ import java.util.Map;
  */
 public class PContactPredictionFile extends AlignFile
 {
+  protected static final String CONTACT_PREDICTION = "CONTACT_PREDICTION";
+
   public PContactPredictionFile(String inFile, DataSourceType fileSourceType)
           throws IOException
   {
@@ -106,7 +108,13 @@ public class PContactPredictionFile extends AlignFile
 
         if (cm == null)
         {
-          cm = new ContactMatrix(true);
+          cm = new ContactMatrix(true) {
+            @Override
+            public String getType()
+            {
+              return CONTACT_PREDICTION;
+            }
+          };
           models.add(cm);
         }
 

diff --git a/src/jalview/renderer/AnnotationRendererFactory.java b/src/jalview/renderer/AnnotationRendererFactory.java
index 1bee418..92ea677 100644 (file)
--- a/src/jalview/renderer/AnnotationRendererFactory.java
+++ b/src/jalview/renderer/AnnotationRendererFactory.java
@@ -31,7 +31,7 @@ public class AnnotationRendererFactory implements
   @Override
   public AnnotationRowRendererI getRendererFor(AlignmentAnnotation row)
   {
-    if (row.graph == AlignmentAnnotation.CUSTOMRENDERER)
+    if (row.graph == AlignmentAnnotation.CONTACT_MAP)
     {
       return new ContactMapRenderer();
     }

diff --git a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
index 272d21d..79ad458 100644 (file)
--- a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
+++ b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
@@ -186,4 +186,11 @@ public class PAEContactMatrix implements ContactMatrixI
   {
     return "pAE Matrix";
   }
+
+  public static final String PAEMATRIX="PAE_MATRIX";
+  @Override
+  public String getType()
+  {
+    return PAEMATRIX;
+  }
 }

diff --git a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
index d2b5aec..8ba2585 100644 (file)
--- a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
+++ b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
@@ -245,7 +245,7 @@ public class DbRefFetcherTest
     assertEquals("One sequence only", resp.getHeight(), 1);
     for (AlignmentAnnotation aa : resp.getAlignmentAnnotation())
     {
-      if (aa.graph == AlignmentAnnotation.CUSTOMRENDERER)
+      if (aa.graph == AlignmentAnnotation.CONTACT_MAP)
       {
         assertTrue("Contact map didn't provide valid contact",
                 resp.getContactListFor(aa, 1).getContactAt(1) != -1d);