Merge branch 'develop' into spike/JAL-4047/JAL-4048_columns_in_sequenceID

[jalview.git] / src / jalview / viewmodel / AlignmentViewport.java

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index e8048e0..7e0b6b4 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -50,6 +50,8 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.ContactListI;
+import jalview.datamodel.ContactMatrixI;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.HiddenSequences;
 import jalview.datamodel.ProfilesI;
@@ -70,6 +72,7 @@ import jalview.util.Comparison;
 import jalview.util.MapList;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
+import jalview.viewmodel.seqfeatures.IdColumns;
 import jalview.viewmodel.styles.ViewStyle;
 import jalview.workers.AlignCalcManager;
 import jalview.workers.ComplementConsensusThread;
@@ -932,7 +935,7 @@ public abstract class AlignmentViewport
     }
     if (calculator.workingInvolvedWith(alignmentAnnotation))
     {
-      // System.err.println("grey out ("+alignmentAnnotation.label+")");
+      // jalview.bin.Console.errPrintln("grey out ("+alignmentAnnotation.label+")");
       return true;
     }
     return false;
@@ -1205,7 +1208,7 @@ public abstract class AlignmentViewport
   {
     if (sequenceSetID != null)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Warning - overwriting a sequenceSetId for a viewport!");
     }
     sequenceSetID = new String(newid);
@@ -2098,7 +2101,7 @@ public abstract class AlignmentViewport
       {
         if (aa == null)
         {
-          System.err.println("Null annotation row: ignoring.");
+          jalview.bin.Console.errPrintln("Null annotation row: ignoring.");
           continue;
         }
         if (!aa.visible)
@@ -2130,7 +2133,7 @@ public abstract class AlignmentViewport
 
         if (aa.graph > 0)
         {
-          aa.height += aa.graphHeight;
+          aa.height += aa.graphHeight+20;
         }
 
         if (aa.height == 0)
@@ -2291,7 +2294,7 @@ public abstract class AlignmentViewport
   {
     if (this == av)
     {
-      System.err.println("Ignoring recursive setCodingComplement request");
+      jalview.bin.Console.errPrintln("Ignoring recursive setCodingComplement request");
     }
     else
     {
@@ -2941,6 +2944,19 @@ public abstract class AlignmentViewport
     return searchResults;
   }
 
+  @Override
+  public ContactListI getContactList(AlignmentAnnotation _aa, int column)
+  {
+    return alignment.getContactListFor(_aa, column);
+  }
+
+  @Override
+  public ContactMatrixI getContactMatrix(
+          AlignmentAnnotation alignmentAnnotation)
+  {
+    return alignment.getContactMatrixFor(alignmentAnnotation);
+  }
+
   /**
    * get the consensus sequence as displayed under the PID consensus annotation
    * row.
@@ -3107,6 +3123,28 @@ public abstract class AlignmentViewport
             false));
   }
 
+  /**
+   * ordered list of annotation values displayed per sequence in ID panel
+   */
+  private IdColumns id_columns = null;
+
+  /**
+   * available and currently visible columns for this view
+   */
+  @Override
+  public IdColumns getIdColumns()
+  {
+    if (alignment == null)
+    {
+      return null;
+    }
+    if (id_columns == null)
+    {
+      id_columns = new IdColumns(alignment);
+    }
+    return id_columns;
+  }
+
   public void setSavedUpToDate(boolean s)
   {
     setSavedUpToDate(s, QuitHandler.Message.UNSAVED_CHANGES);