Merge remote-tracking branch 'origin/develop' into

[jalview.git] / src / jalview / io / AnnotationFile.java

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index ef903e3..e685627 100755 (executable)
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -27,6 +27,7 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.GraphLine;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.HiddenSequences;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
@@ -114,14 +115,12 @@ public class AnnotationFile
 
     public final HiddenSequences hidseqs;
 
-    public final ColumnSelection hiddencols;
-
-    // public final Vector visibleGroups;
+    public final HiddenColumns hiddencols;
 
     public final Hashtable hiddenRepSeqs;
 
     public ViewDef(String vname, HiddenSequences hseqs,
-            ColumnSelection hcols, Hashtable hRepSeqs)
+            HiddenColumns hcols, Hashtable hRepSeqs)
     {
       this.viewname = vname;
       this.hidseqs = hseqs;
@@ -142,7 +141,8 @@ public class AnnotationFile
    */
   public String printAnnotations(AlignmentAnnotation[] annotations,
           List<SequenceGroup> list, Hashtable properties,
-          ColumnSelection cs, AlignmentI al, ViewDef view)
+ HiddenColumns cs,
+          AlignmentI al, ViewDef view)
   {
     if (view != null)
     {
@@ -171,7 +171,7 @@ public class AnnotationFile
     if (cs != null && cs.hasHiddenColumns())
     {
       text.append("VIEW_HIDECOLS\t");
-      List<int[]> hc = cs.getHiddenColumns();
+      List<int[]> hc = cs.getListOfCols();
       boolean comma = false;
       for (int[] r : hc)
       {
@@ -666,15 +666,21 @@ public class AnnotationFile
           String file, DataSourceType protocol)
   {
     ColumnSelection colSel = viewport.getColumnSelection();
+    HiddenColumns hidden = viewport.getAlignment().getHiddenColumns();
     if (colSel == null)
     {
       colSel = new ColumnSelection();
     }
-    boolean rslt = readAnnotationFile(viewport.getAlignment(), colSel,
+    if (hidden == null)
+    {
+      hidden = new HiddenColumns();
+    }
+    boolean rslt = readAnnotationFile(viewport.getAlignment(), hidden,
             file, protocol);
-    if (rslt && (colSel.hasSelectedColumns() || colSel.hasHiddenColumns()))
+    if (rslt && (colSel.hasSelectedColumns() || hidden.hasHiddenColumns()))
     {
       viewport.setColumnSelection(colSel);
+      viewport.getAlignment().setHiddenColumns(hidden);
     }
 
     return rslt;
@@ -686,7 +692,7 @@ public class AnnotationFile
     return readAnnotationFile(al, null, file, sourceType);
   }
 
-  public boolean readAnnotationFile(AlignmentI al, ColumnSelection colSel,
+  public boolean readAnnotationFile(AlignmentI al, HiddenColumns hidden,
           String file, DataSourceType sourceType)
   {
     BufferedReader in = null;
@@ -715,7 +721,7 @@ public class AnnotationFile
       }
       if (in != null)
       {
-        return parseAnnotationFrom(al, colSel, in);
+        return parseAnnotationFrom(al, hidden, in);
       }
 
     } catch (Exception ex)
@@ -738,7 +744,7 @@ public class AnnotationFile
 
   private static String GRAPHLINE = "GRAPHLINE", COMBINE = "COMBINE";
 
-  public boolean parseAnnotationFrom(AlignmentI al, ColumnSelection colSel,
+  public boolean parseAnnotationFrom(AlignmentI al, HiddenColumns hidden,
           BufferedReader in) throws Exception
   {
     nlinesread = 0;
@@ -949,11 +955,11 @@ public class AnnotationFile
         {
           if (st.hasMoreTokens())
           {
-            if (colSel == null)
+            if (hidden == null)
             {
-              colSel = new ColumnSelection();
+              hidden = new HiddenColumns();
             }
-            parseHideCols(colSel, st.nextToken());
+            parseHideCols(hidden, st.nextToken());
           }
           modified = true;
           continue;
@@ -967,7 +973,7 @@ public class AnnotationFile
           }
           if (sr != null)
           {
-            if (colSel == null)
+            if (hidden == null)
             {
               System.err
                       .println("Cannot process HIDE_INSERTIONS without an alignment view: Ignoring line: "
@@ -976,7 +982,7 @@ public class AnnotationFile
             else
             {
               // consider deferring this till after the file has been parsed ?
-              colSel.hideInsertionsFor(sr);
+              hidden.hideInsertionsFor(sr);
             }
           }
           modified = true;
@@ -1182,7 +1188,7 @@ public class AnnotationFile
     return modified;
   }
 
-  private void parseHideCols(ColumnSelection colSel, String nextToken)
+  private void parseHideCols(HiddenColumns hidden, String nextToken)
   {
     StringTokenizer inval = new StringTokenizer(nextToken, ",");
     while (inval.hasMoreTokens())
@@ -1194,7 +1200,7 @@ public class AnnotationFile
         from = to = Integer.parseInt(range);
         if (from >= 0)
         {
-          colSel.hideColumns(from, to);
+          hidden.hideColumns(from, to);
         }
       }
       else
@@ -1210,7 +1216,7 @@ public class AnnotationFile
         }
         if (from > 0 && to >= from)
         {
-          colSel.hideColumns(from, to);
+          hidden.hideColumns(from, to);
         }
       }
     }
@@ -1789,7 +1795,7 @@ public class AnnotationFile
     return printAnnotations(viewport.isShowAnnotation() ? viewport
             .getAlignment().getAlignmentAnnotation() : null, viewport
             .getAlignment().getGroups(), viewport.getAlignment()
-            .getProperties(), viewport.getColumnSelection(),
+            .getProperties(), viewport.getAlignment().getHiddenColumns(),
             viewport.getAlignment(), null);
   }