X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=6c8e0e4e9573b1350249f2bf806649766bd7e4f4;hb=ad35f232acd499d9457056ca24b663866a09edd2;hp=b6094170350b4e4dd2dc7333fd359dd5513bfd8e;hpb=e5f2de91dc41062d8cee8a2a900710f63cf5ae42;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index b609417..6c8e0e4 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -61,6 +61,7 @@ public class AlignViewport
     boolean validCharWidth;
     int wrappedWidth;
     Font font;
+    boolean seqNameItalics;
     AlignmentI alignment;
     ColumnSelection colSel = new ColumnSelection();
     int threshold;
@@ -118,7 +119,9 @@ public class AlignViewport
     Color textColour = Color.black;
     Color textColour2 = Color.white;
 
-    boolean idsAlignRight = false;
+    boolean rightAlignIds = false;
+
+    Hashtable hiddenRepSequences;
 
 
     /**
@@ -158,6 +161,8 @@ public class AlignViewport
       showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
       showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
 
+      rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false);
+
       autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
 
       padGaps = Cache.getDefault("PAD_GAPS", true);
@@ -166,6 +171,8 @@ public class AlignViewport
        String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ;
        String fontSize = Cache.getDefault("FONT_SIZE", "10");
 
+       seqNameItalics = Cache.getDefault("ID_ITALICS", true);
+
        int style = 0;
 
        if (fontStyle.equals("bold"))
@@ -195,6 +202,7 @@ public class AlignViewport
                 11f,
                 AlignmentAnnotation.BAR_GRAPH);
             conservation.hasText = true;
+            conservation.autoCalculated = true;
 
 
             if (Cache.getDefault("SHOW_CONSERVATION", true))
@@ -211,6 +219,7 @@ public class AlignViewport
                                                 11f,
                                                 AlignmentAnnotation.BAR_GRAPH);
               quality.hasText = true;
+              quality.autoCalculated = true;
 
               alignment.addAnnotation(quality);
             }
@@ -220,6 +229,7 @@ public class AlignViewport
                                                new Annotation[1], 0f, 100f,
                                                AlignmentAnnotation.BAR_GRAPH);
           consensus.hasText = true;
+          consensus.autoCalculated = true;
 
            if (Cache.getDefault("SHOW_IDENTITY", true))
            {
@@ -315,7 +325,7 @@ public class AlignViewport
             cons.findQuality();
           }
 
-          String sequence = cons.getConsSequence().getSequence();
+          char [] sequence = cons.getConsSequence().getSequence();
           float minR;
           float minG;
           float minB;
@@ -350,7 +360,7 @@ public class AlignViewport
           {
             float value = 0;
 
-            c = sequence.charAt(i);
+            c = sequence[i];
 
             if (Character.isDigit(c))
               value = (int) (c - '0');
@@ -1260,6 +1270,33 @@ public class AlignViewport
       hasHiddenColumns = true;
     }
 
+    public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
+    {
+      int sSize = sg.getSize();
+      if(sSize < 2)
+        return;
+
+      if(hiddenRepSequences==null)
+        hiddenRepSequences = new Hashtable();
+
+       hiddenRepSequences.put(repSequence, sg);
+
+      //Hide all sequences except the repSequence
+      SequenceI [] seqs = new SequenceI[sSize-1];
+      int index = 0;
+      for(int i=0; i<sSize; i++)
+        if(sg.getSequenceAt(i)!=repSequence)
+        {
+          if(index==sSize-1)
+            return;
+
+          seqs[index++] = sg.getSequenceAt(i);
+        }
+
+      hideSequence(seqs);
+
+    }
+
     public void hideAllSelectedSeqs()
     {
       if (selectionGroup == null)
@@ -1277,8 +1314,9 @@ public class AlignViewport
       if(seq!=null)
       {
         for (int i = 0; i < seq.length; i++)
+        {
           alignment.getHiddenSequences().hideSequence(seq[i]);
-
+        }
         hasHiddenRows = true;
         firePropertyChange("alignment", null, alignment.getSequences());
       }
@@ -1286,7 +1324,8 @@ public class AlignViewport
 
     public void showSequence(int index)
     {
-      Vector tmp = alignment.getHiddenSequences().showSequence(index);
+      Vector tmp = alignment.getHiddenSequences().showSequence(index
+          , hiddenRepSequences);
       if(tmp.size()>0)
       {
         if(selectionGroup==null)
@@ -1330,7 +1369,7 @@ public class AlignViewport
           selectionGroup = new SequenceGroup();
           selectionGroup.setEndRes(alignment.getWidth()-1);
         }
-        Vector tmp = alignment.getHiddenSequences().showAll();
+        Vector tmp = alignment.getHiddenSequences().showAll(hiddenRepSequences);
         for(int t=0; t<tmp.size(); t++)
         {
           selectionGroup.addSequence(
@@ -1339,23 +1378,26 @@ public class AlignViewport
         }
         firePropertyChange("alignment", null, alignment.getSequences());
         hasHiddenRows = false;
+        hiddenRepSequences = null;
       }
     }
 
+
+
     public void invertColumnSelection()
     {
-      int column;
       for(int i=0; i<alignment.getWidth(); i++)
       {
-        column = i;
-
-        if(colSel.contains(column))
-          colSel.removeElement(column);
+        if(colSel.contains(i))
+          colSel.removeElement(i);
         else
-          colSel.addElement(column);
-
+        {
+          if (!hasHiddenColumns || colSel.isVisible(i))
+          {
+            colSel.addElement(i);
+          }
+        }
       }
-
     }
 
     public int adjustForHiddenSeqs(int alignmentIndex)
@@ -1396,7 +1438,7 @@ public class AlignViewport
       int start = 0, end = 0;
       if(selectedRegionOnly && selectionGroup!=null)
       {
-        iSize = selectionGroup.getSize(false);
+        iSize = selectionGroup.getSize();
         seqs = selectionGroup.getSequencesInOrder(alignment);
         start = selectionGroup.getStartRes();
         end = selectionGroup.getEndRes(); // inclusive for start and end in SeqCigar constructor
@@ -1491,7 +1533,7 @@ public class AlignViewport
       int start = 0, end = 0;
       if(selectedRegionOnly && selectionGroup!=null)
       {
-        iSize = selectionGroup.getSize(false);
+        iSize = selectionGroup.getSize();
         seqs = selectionGroup.getSequencesInOrder(alignment);
         start = selectionGroup.getStartRes();
         end = selectionGroup.getEndRes()+1;
@@ -1509,7 +1551,7 @@ public class AlignViewport
       } else {
         for(i=0; i<iSize; i++)
         {
-          selection[i] = seqs[i].getSequence(start, end);
+          selection[i] = seqs[i].getSequenceAsString(start, end);
         }
 
       }
@@ -1563,7 +1605,7 @@ public class AlignViewport
 
         resetAllColourSchemes();
 
-        alignment.adjustSequenceAnnotations();
+       // alignment.adjustSequenceAnnotations();
     }
 
 
@@ -1601,7 +1643,7 @@ public class AlignViewport
         if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
         {
           ((ClustalxColourScheme)sg.cs).resetClustalX(
-              sg.getSequences(true), sg.getWidth());
+              sg.getSequences(hiddenRepSequences), sg.getWidth());
         }
         sg.recalcConservation();
       }