JAL-2526 correct boundary conditions for sequence left/right of cursor

[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 86bb56f..b0210d8 100644 (file)
--- a/src/jalview/ws/jws1/JPredThread.java
+++ b/src/jalview/ws/jws1/JPredThread.java
@@ -27,7 +27,7 @@ import jalview.datamodel.Alignment;
 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;
@@ -38,6 +38,7 @@ import jalview.io.FormatAdapter;
 import jalview.io.IdentifyFile;
 import jalview.io.JPredFile;
 import jalview.io.JnetAnnotationMaker;
+import jalview.io.PileUpfile;
 import jalview.util.Comparison;
 import jalview.util.MessageManager;
 import jalview.ws.AWsJob;
@@ -113,7 +114,7 @@ class JPredThread extends JWS1Thread implements WSClientI
         return null;
       }
       AlignmentI al = null;
-      ColumnSelection alcsel = null;
+      HiddenColumns alhidden = null;
       int FirstSeq = -1; // the position of the query sequence in Alignment al
 
       JpredResult result = (JpredResult) this.result;
@@ -140,10 +141,10 @@ 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];
+            alhidden = (HiddenColumns) alandcolsel[1];
           }
           else
           {
@@ -179,8 +180,8 @@ class JPredThread extends JWS1Thread implements WSClientI
         else
         {
           throw (new Exception(MessageManager.formatMessage(
-                  "exception.unknown_format_for_file", new String[] {
-                      format.toString(), result.getAligfile() })));
+                  "exception.unknown_format_for_file", new String[] { "",
+                      result.getAligfile() })));
         }
       }
       else
@@ -191,7 +192,7 @@ 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(
@@ -236,7 +237,7 @@ class JPredThread extends JWS1Thread implements WSClientI
           {
             // Adjust input view for gaps
             // propagate insertions into profile
-            alcsel = ColumnSelection.propagateInsertions(profileseq, al,
+            alhidden = HiddenColumns.propagateInsertions(profileseq, al,
                     input);
           }
         }
@@ -251,7 +252,7 @@ class JPredThread extends JWS1Thread implements WSClientI
                   alant.sequenceRef);
         }
       }
-      return new Object[] { al, alcsel }; // , FirstSeq, noMsa};
+      return new Object[] { al, alhidden }; // , FirstSeq, noMsa};
     }
 
     /**
@@ -363,8 +364,8 @@ class JPredThread extends JWS1Thread implements WSClientI
         if (msf.length > 1)
         {
           msa = new vamsas.objects.simple.Msfalignment();
-          jalview.io.PileUpfile pileup = new jalview.io.PileUpfile();
-          msa.setMsf(pileup.print(msf));
+          PileUpfile pileup = new PileUpfile();
+          msa.setMsf(pileup.print(msf, true));
         }
       }
     }
@@ -624,7 +625,7 @@ 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
@@ -650,7 +651,8 @@ 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,