JAL-2591 Hidden columns regions can be output to string + test

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

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 9a4071d..b669ee5 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;
@@ -109,23 +110,22 @@ public class AnnotationFile
    */
   public class ViewDef
   {
-    public String viewname;
+    // TODO this class is not used - remove?
+    public final String viewname;
 
-    public HiddenSequences hidseqs;
+    public final HiddenSequences hidseqs;
 
-    public ColumnSelection hiddencols;
+    public final HiddenColumns hiddencols;
 
-    public Vector visibleGroups;
+    public final Hashtable hiddenRepSeqs;
 
-    public Hashtable hiddenRepSeqs;
-
-    public ViewDef(String viewname, HiddenSequences hidseqs,
-            ColumnSelection hiddencols, Hashtable hiddenRepSeqs)
+    public ViewDef(String vname, HiddenSequences hseqs,
+            HiddenColumns hcols, Hashtable hRepSeqs)
     {
-      this.viewname = viewname;
-      this.hidseqs = hidseqs;
-      this.hiddencols = hiddencols;
-      this.hiddenRepSeqs = hiddenRepSeqs;
+      this.viewname = vname;
+      this.hidseqs = hseqs;
+      this.hiddencols = hcols;
+      this.hiddenRepSeqs = hRepSeqs;
     }
   }
 
@@ -141,7 +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)
     {
@@ -151,7 +152,7 @@ public class AnnotationFile
       }
       if (list == null)
       {
-        list = view.visibleGroups;
+        // list = view.visibleGroups;
       }
       if (cs == null)
       {
@@ -170,22 +171,9 @@ public class AnnotationFile
     if (cs != null && cs.hasHiddenColumns())
     {
       text.append("VIEW_HIDECOLS\t");
-      List<int[]> hc = cs.getHiddenColumns();
-      boolean comma = false;
-      for (int[] r : hc)
-      {
-        if (!comma)
-        {
-          comma = true;
-        }
-        else
-        {
-          text.append(",");
-        }
-        text.append(r[0]);
-        text.append("-");
-        text.append(r[1]);
-      }
+
+      String regions = cs.regionsToString(",", "-");
+      text.append(regions);
       text.append("\n");
     }
     // TODO: allow efficient recovery of annotation data shown in several
@@ -201,8 +189,8 @@ public class AnnotationFile
       StringBuffer colours = new StringBuffer();
       StringBuffer graphLine = new StringBuffer();
       StringBuffer rowprops = new StringBuffer();
-      Hashtable<Integer, String> graphGroup = new Hashtable<Integer, String>();
-      Hashtable<Integer, Object[]> graphGroup_refs = new Hashtable<Integer, Object[]>();
+      Hashtable<Integer, String> graphGroup = new Hashtable<>();
+      Hashtable<Integer, Object[]> graphGroup_refs = new Hashtable<>();
       BitSet graphGroupSeen = new BitSet();
 
       java.awt.Color color;
@@ -536,7 +524,7 @@ public class AnnotationFile
     return false;
   }
 
-  public void printGroups(List<SequenceGroup> list)
+  protected void printGroups(List<SequenceGroup> list)
   {
     SequenceI seqrep = null;
     for (SequenceGroup sg : list)
@@ -582,7 +570,8 @@ public class AnnotationFile
       if (sg.cs != null)
       {
         text.append("colour=");
-        text.append(sg.cs.toString());
+        text.append(ColourSchemeProperty.getColourName(sg.cs
+                .getColourScheme()));
         text.append("\t");
         if (sg.cs.getThreshold() != 0)
         {
@@ -664,15 +653,21 @@ 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;
@@ -684,7 +679,7 @@ 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;
@@ -713,7 +708,7 @@ public class AnnotationFile
       }
       if (in != null)
       {
-        return parseAnnotationFrom(al, colSel, in);
+        return parseAnnotationFrom(al, hidden, in);
       }
 
     } catch (Exception ex)
@@ -736,12 +731,12 @@ 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;
-    ArrayList<Object[]> combineAnnotation_calls = new ArrayList<Object[]>();
-    ArrayList<Object[]> deferredAnnotation_calls = new ArrayList<Object[]>();
+    ArrayList<Object[]> combineAnnotation_calls = new ArrayList<>();
+    ArrayList<Object[]> deferredAnnotation_calls = new ArrayList<>();
     boolean modified = false;
     String groupRef = null;
     Hashtable groupRefRows = new Hashtable();
@@ -947,11 +942,11 @@ 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;
@@ -965,7 +960,7 @@ 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: "
@@ -974,7 +969,7 @@ public class AnnotationFile
             else
             {
               // consider deferring this till after the file has been parsed ?
-              colSel.hideInsertionsFor(sr);
+              hidden.hideInsertionsFor(sr);
             }
           }
           modified = true;
@@ -1104,7 +1099,7 @@ public class AnnotationFile
         modified = true;
       }
       // Resolve the groupRefs
-      Hashtable<String, SequenceGroup> groupRefLookup = new Hashtable<String, SequenceGroup>();
+      Hashtable<String, SequenceGroup> groupRefLookup = new Hashtable<>();
       Enumeration en = groupRefRows.keys();
 
       while (en.hasMoreElements())
@@ -1180,7 +1175,7 @@ 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())
@@ -1192,7 +1187,7 @@ public class AnnotationFile
         from = to = Integer.parseInt(range);
         if (from >= 0)
         {
-          colSel.hideColumns(from, to);
+          hidden.hideColumns(from, to);
         }
       }
       else
@@ -1208,7 +1203,7 @@ public class AnnotationFile
         }
         if (from > 0 && to >= from)
         {
-          colSel.hideColumns(from, to);
+          hidden.hideColumns(from, to);
         }
       }
     }
@@ -1787,7 +1782,7 @@ 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);
   }