Check on vscrollMax values

[jalview.git] / src / jalview / appletgui / AlignViewport.java

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