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 33cb9dc..7e0b6b4 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -72,6 +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;
@@ -934,7 +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;
@@ -1207,7 +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);
@@ -2100,7 +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)
@@ -2293,7 +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
     {
@@ -3122,6 +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);