diff --git a/StockholmAlignment.cabal b/StockholmAlignment.cabal
--- a/StockholmAlignment.cabal
+++ b/StockholmAlignment.cabal
@@ -1,11 +1,11 @@
 name:                StockholmAlignment
-version:             1.0.4
+version:             1.1.0
 synopsis:            Libary for Stockholm aligmnent format
 description:         Libary containing parsing and visualisation functions and datastructures for Stockholm aligmnent format
 license:             GPL-3
 license-file:        LICENSE
 author:              Florian Eggenhofer
-maintainer:          egg@tbi.univie.ac.at
+maintainer:          egg@informatik.uni-freiburg.de
 -- copyright:           
 category:            Bioinformatics
 build-type:          Simple
@@ -21,8 +21,8 @@
 
 source-repository this
   type:     git
-  location: https://github.com/eggzilla/StockholmAlignment/tree/1.0.4
-  tag:      1.0.4
+  location: https://github.com/eggzilla/StockholmAlignment/tree/1.1.0
+  tag:      1.1.0
 
 library
   -- Modules exported by the library.
@@ -32,7 +32,7 @@
                      Bio.StockholmFont
 
   -- compiler-options:
-  ghc-options:         -Wall -O2 -fno-warn-unused-do-bind
+  ghc-options:         -Wall -fno-warn-unused-do-bind
 
   -- Other library packages from which modules are imported.
   build-depends:       base >=4.5 && <5, parsec>=3.1.9, diagrams-lib>=1.3, text, vector, ParsecTools, diagrams-cairo>=1.3, filepath, colour, directory, either-unwrap, SVGFonts >= 1.4
diff --git a/changelog b/changelog
--- a/changelog
+++ b/changelog
@@ -1,4 +1,7 @@
 -*-change-log-*-
+1.1.0 Florian Eggenhofer <egg@informatik.uni-freiburg.de> 7. May 2017
+	* Specific column labels are now passed as color vectors independent of model indices
+	* Added consensus secondary structure to alignment visualisation
 1.0.4 Florian Eggenhofer <egg@informatik.uni-freiburg.de> 27. April 2017
         * Added visualisation of consensus secondary structure if present
 1.0.3 Florian Eggenhofer <egg@informatik.uni-freiburg.de> 24. April 2017
diff --git a/src/Bio/StockholmDraw.hs b/src/Bio/StockholmDraw.hs
--- a/src/Bio/StockholmDraw.hs
+++ b/src/Bio/StockholmDraw.hs
@@ -10,6 +10,7 @@
      drawStockholm,
      convertWUSStoDotBracket,
      extractGapfreeStructure,
+     extractGapfreeIndexedStructure,
      isGap
     ) where
 
@@ -23,8 +24,8 @@
 import Graphics.SVGFonts
 import Bio.StockholmFont
 
-drawStockholmLines :: Int -> Double -> V.Vector Int -> V.Vector (Int, V.Vector (Colour Double)) -> S.StockholmAlignment -> QDiagram Cairo V2 Double Any
-drawStockholmLines entriesNumberCutoff maxWidth nodeAlignmentColIndices comparisonNodeLabels aln = alignmentBlocks
+drawStockholmLines :: Int -> Double -> V.Vector (Int, V.Vector (Colour Double)) -> S.StockholmAlignment -> QDiagram Cairo V2 Double Any
+drawStockholmLines entriesNumberCutoff maxWidth columnComparisonLabels aln = alignmentBlocks
   where seqEntries = V.fromList (take entriesNumberCutoff (S.sequenceEntries aln))
         --consensusStructureEntry = if null (S.columnAnnotations aln) then mempty else drawConsensusStructureEntry maxIdLength (S.columnAnnotations aln)
         maybeConsensusStructureEntry = find ((T.pack "SS_cons"==) . S.tag) (S.columnAnnotations aln)
@@ -37,9 +38,9 @@
         letterWidth = 2.0 :: Double
         availableLettersPerRow = maxWidth / letterWidth
         blocks = makeLetterIntervals entryNumber availableLettersPerRow maxEntryLength
-        colIndicescomparisonNodeLabels = V.zipWith (\a b -> (a,b)) nodeAlignmentColIndices comparisonNodeLabels
-        sparseComparisonColLabels = V.map nodeToColIndices colIndicescomparisonNodeLabels
-        fullComparisonColLabels = fillComparisonColLabels maxEntryLength sparseComparisonColLabels
+        --colIndicescomparisonNodeLabels = V.zipWith (\a b -> (a,b)) nodeAlignmentColIndices comparisonNodeLabels
+        --sparseComparisonColLabels = V.map nodeToColIndices colIndicescomparisonNodeLabels
+        fullComparisonColLabels = fillComparisonColLabels maxEntryLength columnComparisonLabels
         alignmentBlocks = vcat' with { _sep = 6.0 } (map (drawStockholmRowBlock maxIdLength vectorEntries maxEntryLength fullComparisonColLabels) blocks)  
         
 extractGapfreeStructure :: String -> String -> String
@@ -55,6 +56,20 @@
         gapfreeCompleteStructure = V.filter (\(i,_) -> notElem i sequencegaps) (V.indexed completeBPStructure)
         entryStructure = map snd (V.toList  gapfreeCompleteStructure)
 
+
+extractGapfreeIndexedStructure :: String -> String -> [(Int,Char)]
+extractGapfreeIndexedStructure alignedSequence regularStructure1 = indexedEntryStructure
+  where regularsequence1 = map convertToRegularGap alignedSequence
+        bpindicestest1 = basePairIndices regularStructure1 [] 0
+        sequencegaps = elemIndices '-' regularsequence1
+        -- convert incomplete basepairs to .
+        incompleteBasepairs = filter (\(i,j) -> elem i sequencegaps || elem j sequencegaps) bpindicestest1
+        incompleteIndicesCharacterPairs = concatMap (\(a,b) -> [(a,'.'),(b,'.')]) incompleteBasepairs
+        completeBPStructure = V.update (V.fromList regularStructure1) (V.fromList incompleteIndicesCharacterPairs)
+        -- remove gap character postitions from structure string
+        gapfreeCompleteStructure = V.filter (\(i,_) -> notElem i sequencegaps) (V.indexed completeBPStructure)
+        indexedEntryStructure = (V.toList gapfreeCompleteStructure)        
+
 basePairIndices :: String -> [Int] -> Int -> [(Int,Int)]
 basePairIndices (x:xs) ys counter
   | x == '(' = basePairIndices xs (counter:ys) (counter+1)
@@ -98,10 +113,6 @@
   | c == ':' = '.'
   | c == ',' = '.'
   | otherwise = c
-
-
-nodeToColIndices :: (Int,(Int,V.Vector (Colour Double))) -> (Int,V.Vector (Colour Double))
-nodeToColIndices (colIndex,(_,colors)) = (colIndex,colors)
 
 fillComparisonColLabels :: Int ->  V.Vector (Int, V.Vector (Colour Double)) ->  V.Vector (Int, V.Vector (Colour Double))
 fillComparisonColLabels maxEntryLength sparseComparisonColLabels = fullComparisonColLabels