X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=350921722fa2d3a56ac8053787e15543340f1841;hb=6fc9aca27f606f6e3a0121597896e1a5dae35c36;hp=cb977d0de63c59c6d8ecbd45473feef06bbc75dd;hpb=7ebd4d6015b795c76cdc3eef274dae402b6ba5b7;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index cb977d0..3509217 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -62,7 +62,7 @@ public class AlignViewport
     int charHeight;
     int charWidth;
     int wrappedWidth;
-    Font font = new Font("SansSerif", Font.PLAIN, 10);
+    Font font;
     AlignmentI alignment;
     ColumnSelection colSel = new ColumnSelection();
     int threshold;
@@ -72,6 +72,9 @@ public class AlignViewport
     boolean scaleLeftWrapped = true;
     boolean scaleRightWrapped = true;
     boolean hasHiddenColumns = false;
+    boolean hasHiddenRows = false;
+
+    boolean cursorMode = false;
 
     // The following vector holds the features which are
     // currently visible, in the correct order or rendering
@@ -83,6 +86,7 @@ public class AlignViewport
     AlignmentAnnotation consensus;
     AlignmentAnnotation conservation;
     AlignmentAnnotation quality;
+    boolean autoCalculateConsensus = true;
 
     /** DOCUMENT ME!! */
     public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
@@ -96,6 +100,8 @@ public class AlignViewport
 
     boolean antiAlias = false;
 
+    boolean padGaps = false;
+
 
     public AlignViewport(AlignmentI al, boolean dataset)
     {
@@ -130,6 +136,10 @@ public class AlignViewport
       showQuality = Cache.getDefault("SHOW_QUALITY", true);
       showIdentity = Cache.getDefault("SHOW_IDENTITY", true);
 
+      autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
+
+      padGaps = Cache.getDefault("PAD_GAPS", false);
+
        String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
        String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ;
        String fontSize = Cache.getDefault("FONT_SIZE", "10");
@@ -1075,7 +1085,6 @@ public class AlignViewport
       {
         globalColourScheme.setThreshold(globalColourScheme.getThreshold(), ignoreGapsInConsensusCalculation);
       }
-
     }
 
     public boolean getIgnoreGapsConsensus()
@@ -1092,4 +1101,23 @@ public class AlignViewport
     {
       return isDataset;
     }
+
+    public void hideSequence(SequenceI seq)
+    {
+      alignment.getHiddenSequences().hideSequence(seq);
+      hasHiddenRows = true;
+    }
+
+    public void showSequence(int index)
+    {
+      alignment.getHiddenSequences().showSequence(index);
+
+      if(alignment.getHiddenSequences().getSize()<1)
+        hasHiddenRows = false;
+    }
+
+    public int adjustForHiddenSeqs(int alignmentIndex)
+    {
+      return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);
+    }
 }