X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=fc4638697a6fd6b9cd96f5b0391285fd4c5b708d;hb=7be3a744db5213f49e70178ade126d1cc797c762;hp=7c46cd9b492dd4646d55817780a55d2da9b12dc0;hpb=b169b1a49c078d123feb729db6acb9779f50e7d6;p=jalview.git

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 7c46cd9..fc46386 100755
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -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;
@@ -101,6 +102,8 @@ public class AlignViewport
 
   jalview.bin.JalviewLite applet;
 
+  boolean MAC = false;
+
   public AlignViewport(AlignmentI al, JalviewLite applet)
   {
     this.applet = applet;
@@ -111,6 +114,9 @@ public class AlignViewport
     this.endSeq = al.getHeight() - 1;
     setFont(font);
 
+    if(System.getProperty("os.name").startsWith("Mac"))
+      MAC = true;
+
     if (applet != null)
     {
       String param = applet.getParameter("showFullId");
@@ -142,6 +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
@@ -352,7 +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;
@@ -462,7 +501,14 @@ public class AlignViewport
 
     java.awt.FontMetrics fm = nullFrame.getGraphics().getFontMetrics(font);
     setCharHeight(fm.getHeight());
-    setCharWidth(fm.charWidth('M'));
+    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()
@@ -470,11 +516,6 @@ public class AlignViewport
     return font;
   }
 
-  public void setCharWidth(int w)
-  {
-    this.charWidth = w;
-  }
-
   public int getCharWidth()
   {
     return charWidth;
@@ -760,39 +801,32 @@ public class AlignViewport
       colSel.hideColumns(start);
     else
       colSel.hideColumns(start, end);
-    setSelectionGroup(null);
+
     hasHiddenColumns = true;
   }
 
-  public void hideSequence(SequenceI seq)
+  public void hideAllSelectedSeqs()
   {
-    if(seq!=null)
-    {
-      alignment.getHiddenSequences().hideSequence(seq);
-      hasHiddenRows = true;
-    }
+    if (selectionGroup == null)
+      return;
+
+    SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
+
+    hideSequence(seqs);
+
+    setSelectionGroup(null);
   }
 
-  public void showSequence(int index)
+  public void hideSequence(SequenceI [] seq)
   {
-    Vector tmp = alignment.getHiddenSequences().showSequence(index);
-    if (tmp.size() > 0)
+    if(seq!=null)
     {
-      if (selectionGroup == null)
-      {
-        selectionGroup = new SequenceGroup();
-        selectionGroup.setEndRes(alignment.getWidth() - 1);
-      }
+      for (int i = 0; i < seq.length; i++)
+        alignment.getHiddenSequences().hideSequence(seq[i]);
 
-      for (int t = 0; t < tmp.size(); t++)
-      {
-        selectionGroup.addSequence(
-            (SequenceI) tmp.elementAt(t), false
-            );
-      }
+      hasHiddenRows = true;
+      firePropertyChange("alignment", null, alignment.getSequences());
     }
-    if (alignment.getHiddenSequences().getSize() < 1)
-      hasHiddenRows = false;
   }
 
   public void showColumn(int col)
@@ -824,8 +858,9 @@ public class AlignViewport
             (SequenceI)tmp.elementAt(t), false
             );
       }
+      firePropertyChange("alignment", null, alignment.getSequences());
       hasHiddenRows = false;
-      }
+    }
   }
 
   public int adjustForHiddenSeqs(int alignmentIndex)
@@ -921,9 +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;
   }