X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=fc4638697a6fd6b9cd96f5b0391285fd4c5b708d;hb=8240aa86ee94d4c372af7deb1452a8294ff8800b;hp=0013bc05c882055848e92f74afcb53446eaa25d7;hpb=502eab512b790bcee60cefef90b0c46711a4264d;p=jalview.git

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 0013bc0..fc46386 100755
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -50,6 +50,7 @@ public class AlignViewport
   boolean showConservation = true;
   boolean showQuality = true;
   boolean showConsensus = true;
+  boolean upperCasebold = false;
 
   boolean colourAppliesToAllGroups = true;
   ColourSchemeI globalColourScheme = null;
@@ -79,7 +80,7 @@ public class AlignViewport
 
   // The following vector holds the features which are
  // currently visible, in the correct order or rendering
-  Hashtable featuresDisplayed;
+  public Hashtable featuresDisplayed;
 
   boolean hasHiddenColumns = false;
   boolean hasHiddenRows = false;
@@ -147,6 +148,14 @@ public class AlignViewport
       {
         showConsensus = Boolean.valueOf(param).booleanValue();
       }
+
+      param = applet.getParameter("upperCase");
+      if (param != null)
+      {
+        if(param.equalsIgnoreCase("bold"))
+          upperCasebold = true;
+      }
+
     }
     // We must set conservation and consensus before setting colour,
     // as Blosum and Clustal require this to be done
@@ -357,7 +366,32 @@ public class AlignViewport
           globalColourScheme.setConsensus(vconsensus);
 
   }
-
+  /**
+   * get the consensus sequence as displayed under the PID consensus annotation row.
+   * @return consensus sequence as a new sequence object
+   */
+  /**
+   * get the consensus sequence as displayed under the PID consensus annotation row.
+   * @return consensus sequence as a new sequence object
+   */
+  public SequenceI getConsensusSeq() {
+    if (consensus==null)
+      updateConsensus();
+    if (consensus==null)
+      return null;
+    StringBuffer seqs=new StringBuffer();
+    for (int i=0; i<consensus.annotations.length; i++) {
+      if (consensus.annotations[i]!=null) {
+        if (consensus.annotations[i].description.charAt(0) == '[')
+          seqs.append(consensus.annotations[i].description.charAt(1));
+        else
+          seqs.append(consensus.annotations[i].displayCharacter);
+      }
+    }
+    SequenceI sq = new Sequence("Consensus", seqs.toString());
+    sq.setDescription("Percentage Identity Consensus "+((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
+    return sq;
+  }
   public SequenceGroup getSelectionGroup()
   {
     return selectionGroup;
@@ -468,6 +502,13 @@ public class AlignViewport
     java.awt.FontMetrics fm = nullFrame.getGraphics().getFontMetrics(font);
     setCharHeight(fm.getHeight());
     charWidth = fm.charWidth('M');
+
+    if(upperCasebold)
+    {
+      Font f2 = new Font(f.getName(), Font.BOLD, f.getSize());
+      fm = nullFrame.getGraphics().getFontMetrics(f2);
+      charWidth = fm.stringWidth("MMMMMMMMMMM") / 10;
+    }
   }
 
   public Font getFont()
@@ -764,16 +805,6 @@ public class AlignViewport
     hasHiddenColumns = true;
   }
 
-  public void hideSequence(SequenceI seq)
-  {
-    if(seq!=null)
-    {
-      alignment.getHiddenSequences().hideSequence(seq);
-      hasHiddenRows = true;
-      firePropertyChange("alignment", null, alignment.getSequences());
-    }
-  }
-
   public void hideAllSelectedSeqs()
   {
     if (selectionGroup == null)
@@ -781,13 +812,21 @@ public class AlignViewport
 
     SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
 
-    for (int i = 0; i < seqs.length; i++)
+    hideSequence(seqs);
+
+    setSelectionGroup(null);
+  }
+
+  public void hideSequence(SequenceI [] seq)
+  {
+    if(seq!=null)
     {
-      alignment.getHiddenSequences().hideSequence(seqs[i]);
+      for (int i = 0; i < seq.length; i++)
+        alignment.getHiddenSequences().hideSequence(seq[i]);
+
+      hasHiddenRows = true;
+      firePropertyChange("alignment", null, alignment.getSequences());
     }
-    firePropertyChange("alignment", null, alignment.getSequences());
-    hasHiddenRows = true;
-    setSelectionGroup(null);
   }
 
   public void showColumn(int col)
@@ -917,9 +956,9 @@ public class AlignViewport
       }
       // Final match if necessary.
       if (last<end)
-        selection.addOperation(CigarArray.M, end-last);
+        selection.addOperation(CigarArray.M, end-last+1);
     } else {
-      selection.addOperation(CigarArray.M, end-start);
+      selection.addOperation(CigarArray.M, end-start+1);
     }
     return selection;
   }