JAL-2388 Hidden cols separated from column selection (almost complete)

[jalview.git] / src / jalview / ws / jws1 / JPredThread.java

diff --git a/src/jalview/ws/jws1/JPredThread.java b/src/jalview/ws/jws1/JPredThread.java
index e685d00..078f189 100644 (file)
--- a/src/jalview/ws/jws1/JPredThread.java
+++ b/src/jalview/ws/jws1/JPredThread.java
@@ -28,6 +28,7 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
@@ -141,7 +142,7 @@ class JPredThread extends JWS1Thread implements WSClientI
           if (predMap != null)
           {
             Object[] alandcolsel = input
-                    .getAlignmentAndColumnSelection(getGapChar());
+                    .getAlignmentAndHiddenColumns(getGapChar());
             sqs = (SequenceI[]) alandcolsel[0];
             al = new Alignment(sqs);
             alcsel = (ColumnSelection) alandcolsel[1];
@@ -192,7 +193,7 @@ class JPredThread extends JWS1Thread implements WSClientI
         {
           char gc = getGapChar();
           SequenceI[] sqs = (SequenceI[]) input
-                  .getAlignmentAndColumnSelection(gc)[0];
+                  .getAlignmentAndHiddenColumns(gc)[0];
           if (this.msaIndex >= sqs.length)
           {
             throw new Error(
@@ -625,7 +626,7 @@ class JPredThread extends JWS1Thread implements WSClientI
             if (res[1] != null)
             {
               af = new AlignFrame((Alignment) res[0],
-                      (ColumnSelection) res[1], AlignFrame.DEFAULT_WIDTH,
+                      (HiddenColumns) res[1], AlignFrame.DEFAULT_WIDTH,
                       AlignFrame.DEFAULT_HEIGHT);
             }
             else
@@ -651,7 +652,8 @@ class JPredThread extends JWS1Thread implements WSClientI
              */
 
             af = new AlignFrame((Alignment) res[0],
-                    (ColumnSelection) res[1], AlignFrame.DEFAULT_WIDTH,
+ (HiddenColumns) res[1],
+                    AlignFrame.DEFAULT_WIDTH,
                     AlignFrame.DEFAULT_HEIGHT);
           }
           Desktop.addInternalFrame(af, altitle, AlignFrame.DEFAULT_WIDTH,