show hide stuff moved from columnSelection

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 2e1a4e0..a101fcf 100755 (executable)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -74,6 +74,7 @@ public class AlignViewport
     boolean scaleRightWrapped = true;\r
     boolean hasHiddenColumns = false;\r
     boolean hasHiddenRows = false;\r
+    boolean showHiddenMarkers = true;\r
 \r
     boolean cursorMode = false;\r
 \r
@@ -1119,10 +1120,44 @@ public class AlignViewport
       return isDataset;\r
     }\r
 \r
+\r
+    public void hideSelectedColumns()\r
+    {\r
+      if (colSel.selected.size() < 1)\r
+        return;\r
+\r
+      while (colSel.selected.size() > 0)\r
+      {\r
+        int column = ( (Integer) colSel.selected.firstElement()).intValue();\r
+        colSel.hideColumns(column);\r
+      }\r
+      setSelectionGroup(null);\r
+      hasHiddenColumns = true;\r
+    }\r
+\r
+\r
+    public void hideColumns(int start, int end)\r
+    {\r
+      if(start==end)\r
+        end++;\r
+\r
+      for(int i=start; i<end; i++)\r
+      {\r
+        colSel.addElement(i);\r
+        colSel.hideColumns(i);\r
+      }\r
+\r
+      setSelectionGroup(null);\r
+      hasHiddenColumns = true;\r
+    }\r
+\r
     public void hideSequence(SequenceI seq)\r
     {\r
-      alignment.getHiddenSequences().hideSequence(seq);\r
-      hasHiddenRows = true;\r
+      if(seq!=null)\r
+      {\r
+        alignment.getHiddenSequences().hideSequence(seq);\r
+        hasHiddenRows = true;\r
+      }\r
     }\r
 \r
     public void showSequence(int index)\r
@@ -1135,8 +1170,11 @@ public class AlignViewport
 \r
     public void showAllHiddenSeqs()\r
     {\r
-      alignment.getHiddenSequences().showAll();\r
-      hasHiddenRows = false;\r
+      if(alignment.getHiddenSequences().getSize()>0)\r
+      {\r
+        alignment.getHiddenSequences().showAll();\r
+        hasHiddenRows = false;\r
+      }\r
     }\r
 \r
     public int adjustForHiddenSeqs(int alignmentIndex)\r
@@ -1245,4 +1283,14 @@ public class AlignViewport
 \r
       return selection;\r
     }\r
+\r
+    public boolean getShowHiddenMarkers()\r
+    {\r
+      return showHiddenMarkers;\r
+    }\r
+\r
+    public void setShowHiddenMarkers(boolean show)\r
+    {\r
+      showHiddenMarkers = show;\r
+    }\r
 }\r

diff --git a/src/jalview/gui/ColumnSelection.java b/src/jalview/gui/ColumnSelection.java
index eb6cafe..94e2642 100755 (executable)
--- a/src/jalview/gui/ColumnSelection.java
+++ b/src/jalview/gui/ColumnSelection.java
@@ -330,7 +330,8 @@ public class ColumnSelection
     }\r
 \r
 \r
-    public void hideColumns(int res, AlignViewport av)\r
+\r
+    public void hideColumns(int res)\r
     {\r
       if(hiddenColumns==null)\r
         hiddenColumns = new Vector();\r
@@ -360,19 +361,19 @@ public class ColumnSelection
       if(!added)\r
         hiddenColumns.addElement(new int[]{min, max});\r
 \r
-\r
-      av.setSelectionGroup(null);\r
-      av.hasHiddenColumns = true;\r
     }\r
 \r
     public void revealAllHiddenColumns(AlignViewport av)\r
     {\r
-      for(int i=0; i<hiddenColumns.size(); i++)\r
+      if(hiddenColumns!=null)\r
       {\r
-        int [] region = (int[])hiddenColumns.elementAt(i);\r
-        for(int j=region[0]; j<region[1]; j++)\r
+        for (int i = 0; i < hiddenColumns.size(); i++)\r
         {\r
-          addElement(j);\r
+          int[] region = (int[]) hiddenColumns.elementAt(i);\r
+          for (int j = region[0]; j < region[1]; j++)\r
+          {\r
+            addElement(j);\r
+          }\r
         }\r
       }\r
       av.hasHiddenColumns = false;\r