X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=350921722fa2d3a56ac8053787e15543340f1841;hb=6fc9aca27f606f6e3a0121597896e1a5dae35c36;hp=7f8675375da91f3acaba5922e27fde0170325f5e;hpb=9c5d69ef1e102b1eac18ec13c362522f40c9000d;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 7f86753..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;
@@ -71,12 +71,22 @@ public class AlignViewport
     boolean scaleAboveWrapped = false;
     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
+    Hashtable featuresDisplayed = null;
+
 
     /** DOCUMENT ME!! */
     public Vector vconsensus;
     AlignmentAnnotation consensus;
     AlignmentAnnotation conservation;
     AlignmentAnnotation quality;
+    boolean autoCalculateConsensus = true;
 
     /** DOCUMENT ME!! */
     public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
@@ -88,6 +98,10 @@ public class AlignViewport
 
     boolean isDataset = false;
 
+    boolean antiAlias = false;
+
+    boolean padGaps = false;
+
 
     public AlignViewport(AlignmentI al, boolean dataset)
     {
@@ -113,6 +127,8 @@ public class AlignViewport
         this.startSeq = 0;
         this.endSeq = alignment.getHeight() - 1;
 
+      antiAlias = Cache.getDefault("ANTI_ALIAS", false);
+
       showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
       showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
       showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
@@ -120,6 +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");
@@ -174,11 +194,16 @@ public class AlignViewport
      *
      * @param b DOCUMENT ME!
      */
-    public void showSequenceFeatures(boolean b)
+    public void setShowSequenceFeatures(boolean b)
     {
         showSequenceFeatures = b;
     }
 
+    public boolean getShowSequenceFeatures()
+    {
+      return showSequenceFeatures;
+    }
+
     /**
      * DOCUMENT ME!
      */
@@ -264,7 +289,7 @@ public class AlignViewport
                                                  ConsPercGaps + "% gaps",
                                                  annotations, 0f, // cons.qualityRange[0].floatValue(),
                                                  11f, // cons.qualityRange[1].floatValue()
-                                                 1);
+                                                 AlignmentAnnotation.BAR_GRAPH);
 
           if (showConservation)
           {
@@ -276,7 +301,7 @@ public class AlignViewport
                                             qannotations,
                                             cons.qualityRange[0].floatValue(),
                                             cons.qualityRange[1].floatValue(),
-                                            1);
+                                            AlignmentAnnotation.BAR_GRAPH);
 
           if (showQuality)
           {
@@ -360,7 +385,7 @@ public class AlignViewport
         if (consensus == null)
         {
           consensus = new AlignmentAnnotation("Consensus", "PID",
-                                              annotations, 0f, 100f, 1);
+                                              annotations, 0f, 100f,AlignmentAnnotation.BAR_GRAPH);
 
           if (showIdentity)
           {
@@ -1060,7 +1085,6 @@ public class AlignViewport
       {
         globalColourScheme.setThreshold(globalColourScheme.getThreshold(), ignoreGapsInConsensusCalculation);
       }
-
     }
 
     public boolean getIgnoreGapsConsensus()
@@ -1077,4 +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);
+    }
 }