From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 30 Mar 2018 14:56:41 +0000 (+0100)
Subject: Updated with latest from mchmmer branch
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=04a4d60a50394d846d0479c442facebe360b5b9c;p=jalview.git

Updated with latest from mchmmer branch
---

diff --git a/.classpath b/.classpath
index c85feaf..896611c 100644
--- a/.classpath
+++ b/.classpath
@@ -69,5 +69,6 @@
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8"/>
 	<classpathentry kind="lib" path="lib/htsjdk-2.12.0.jar"/>
 	<classpathentry kind="lib" path="lib/groovy-all-2.4.12-indy.jar"/>
+	<classpathentry exported="true" kind="con" path="GROOVY_DSL_SUPPORT"/>
 	<classpathentry kind="output" path="classes"/>
 </classpath>
diff --git a/RELEASE b/RELEASE
index eb9d7cd..5ad87c8 100644
--- a/RELEASE
+++ b/RELEASE
@@ -1,2 +1,2 @@
-jalview.release=releases/Release_2_10_3_Branch
-jalview.version=2.10.3b1
+jalview.release=releases/Release_2_10_4_Branch
+jalview.version=2.10.4
diff --git a/benchmarking/README b/benchmarking/README
index ccf53c1..d1ec146 100644
--- a/benchmarking/README
+++ b/benchmarking/README
@@ -27,6 +27,9 @@ to install the jalview.jar file in the local maven repository. The pom.xml in th
   To get JSON output instead use:
   java -jar target/benchmarks.jar -rf json
   
+  To run a specific benchmark file use:
+  java -jar target/benchmarks.jar <Benchmark class name> 
+  
   JSON output can be viewed quickly by drag-dropping on http://jmh.morethan.io/
   
   To get help use the standard -h option:
@@ -38,3 +41,4 @@ to install the jalview.jar file in the local maven repository. The pom.xml in th
   
   
  6. If you make changes to the Jalview code everything will need to be refreshed, by performing steps 3-5 again.
+
diff --git a/benchmarking/src/main/java/org/jalview/HiddenColumnsBenchmark.java b/benchmarking/src/main/java/org/jalview/HiddenColumnsBenchmark.java
index d3c67d7..07b76f9 100644
--- a/benchmarking/src/main/java/org/jalview/HiddenColumnsBenchmark.java
+++ b/benchmarking/src/main/java/org/jalview/HiddenColumnsBenchmark.java
@@ -47,128 +47,111 @@ import jalview.datamodel.HiddenColumns;
 @Measurement(iterations = 10, time = 500, timeUnit = TimeUnit.MILLISECONDS)
 @Fork(1)
 public class HiddenColumnsBenchmark 
-{
-  /*
-   * State with multiple hidden columns and a start position set
-   */
-  @State(Scope.Thread)
-  public static class HiddenColsAndStartState
-  {
-    @Param({ "300", "10000", "100000" })
-    public int maxcols;
-
-    @Param({ "1", "50", "90" })
-    public int startpcnt; // position as percentage of maxcols
-
-    @Param({ "1", "15", "100" })
-    public int hide;
-
-    HiddenColumns h = new HiddenColumns();
-
-    Random rand = new Random();
-
-    public int hiddenColumn;
-
-    public int visibleColumn;
-
-    @Setup
-    public void setup()
+{	
+	/*
+	 * State with multiple hidden columns and a start position set
+	 */
+	@State(Scope.Thread)
+	public static class HiddenColsAndStartState
+	{
+		@Param({"100", "1000", "10000", "100000", "1000000"})
+		public int maxcols;
+		
+		@Param({"1", "50", "90"})
+		public int startpcnt; // position as percentage of maxcols
+		
+		@Param({"1","15","100"})
+		public int hide;
+		
+		HiddenColumns h = new HiddenColumns();
+		Random rand = new Random();
+		
+		public int hiddenColumn;
+		public int visibleColumn;
+	
+		@Setup
+		public void setup()
+		{
+			rand.setSeed(1234);
+			int lastcol = 0;
+	    	while (lastcol < maxcols)
+	    	{
+	    		int count = rand.nextInt(100); 
+	    		lastcol += count;
+	    		h.hideColumns(lastcol, lastcol+hide);
+	    		lastcol+=hide;
+	    	}
+	    	
+	    	// make sure column at start is hidden
+	    	hiddenColumn = (int)(maxcols * startpcnt/100.0);
+	    	h.hideColumns(hiddenColumn, hiddenColumn);
+	    	
+	    	// and column <hide> after start is visible
+	    	ColumnSelection sel = new ColumnSelection();
+	    	h.revealHiddenColumns(hiddenColumn+hide, sel);
+	    	visibleColumn = hiddenColumn+hide;
+	    	
+	    	System.out.println("Maxcols: " + maxcols + " HiddenCol: " + hiddenColumn + " Hide: " + hide);
+	    	System.out.println("Number of hidden columns: " + h.getSize());
+		}
+	}
+	
+	/* Convention: functions in alphabetical order */
+	
+	@Benchmark
+	@BenchmarkMode({Mode.Throughput})
+	public int benchAdjustForHiddenColumns(HiddenColsAndStartState tstate)
+	{
+		return tstate.h.visibleToAbsoluteColumn(tstate.visibleColumn);
+	}
+	
+	@Benchmark
+	@BenchmarkMode({Mode.Throughput})
+	public int benchFindColumnPosition(HiddenColsAndStartState tstate)
+	{
+		return tstate.h.absoluteToVisibleColumn(tstate.visibleColumn);
+	}
+	
+	@Benchmark
+	@BenchmarkMode({Mode.Throughput})
+    public int benchGetSize(HiddenColsAndStartState tstate)
     {
-      rand.setSeed(1234);
-      int lastcol = 0;
-      while (lastcol < maxcols)
-      {
-        int count = rand.nextInt(100);
-        lastcol += count;
-        h.hideColumns(lastcol, lastcol + hide);
-        lastcol += hide;
-      }
-
-      // make sure column at start is hidden
-      hiddenColumn = (int) (maxcols * startpcnt / 100.0);
-      h.hideColumns(hiddenColumn, hiddenColumn);
-
-      // and column <hide> after start is visible
-      ColumnSelection sel = new ColumnSelection();
-      h.revealHiddenColumns(hiddenColumn + hide, sel);
-      visibleColumn = hiddenColumn + hide;
-
-      System.out.println("Maxcols: " + maxcols + " HiddenCol: "
-              + hiddenColumn + " Hide: " + hide);
-      System.out.println("Number of hidden columns: " + h.getSize());
+		return tstate.h.getSize();
     }
-  }
-
-  /* Convention: functions in alphabetical order */
-
-  @Benchmark
-  @BenchmarkMode({ Mode.Throughput })
-  public int benchAdjustForHiddenColumns(HiddenColsAndStartState tstate)
-  {
-    return tstate.h.adjustForHiddenColumns(tstate.visibleColumn);
-  }
-
-  @Benchmark
-  @BenchmarkMode({ Mode.Throughput })
-  public int benchFindColumnPosition(HiddenColsAndStartState tstate)
-  {
-    return tstate.h.findColumnPosition(tstate.visibleColumn);
-  }
-
-  @Benchmark
-  @BenchmarkMode({ Mode.Throughput })
-  public List<Integer> benchFindHiddenRegionPositions(
-          HiddenColsAndStartState tstate)
-  {
-    return tstate.h.findHiddenRegionPositions();
-  }
-
-  @Benchmark
-  @BenchmarkMode({ Mode.Throughput })
-  public ArrayList<int[]> benchGetHiddenColumnsCopy(
-          HiddenColsAndStartState tstate)
-  {
-    return tstate.h.getHiddenColumnsCopy();
-  }
-
-  @Benchmark
-  @BenchmarkMode({ Mode.Throughput })
-  public int benchGetSize(HiddenColsAndStartState tstate)
-  {
-    return tstate.h.getSize();
-  }
-
-  @Benchmark
-  @BenchmarkMode({ Mode.Throughput })
-  public HiddenColumns benchHideCols(HiddenColsAndStartState tstate)
-  {
-    tstate.h.hideColumns(tstate.visibleColumn, tstate.visibleColumn + 2000);
-    return tstate.h;
-  }
-
-  @Benchmark
-  @BenchmarkMode({ Mode.Throughput })
-  public boolean benchIsVisible(HiddenColsAndStartState tstate)
-  {
-    return tstate.h.isVisible(tstate.hiddenColumn);
-  }
-
-  @Benchmark
-  @BenchmarkMode({ Mode.Throughput })
-  public HiddenColumns benchReveal(HiddenColsAndStartState tstate)
-  {
-    ColumnSelection sel = new ColumnSelection();
-    tstate.h.revealHiddenColumns(tstate.hiddenColumn, sel);
-    return tstate.h;
-  }
-
-  @Benchmark
-  @BenchmarkMode({ Mode.Throughput })
-  public HiddenColumns benchRevealAll(HiddenColsAndStartState tstate)
-  {
-    ColumnSelection sel = new ColumnSelection();
-    tstate.h.revealAllHiddenColumns(sel);
-    return tstate.h;
-  }
 
+   @Benchmark
+    @BenchmarkMode({Mode.Throughput})
+    public HiddenColumns benchHideCols(HiddenColsAndStartState tstate) 
+    {
+    	tstate.h.hideColumns(tstate.visibleColumn,
+    			tstate.visibleColumn+2000); 
+    	return tstate.h;
+    }
+   
+	@Benchmark
+	@BenchmarkMode({Mode.Throughput})
+    public boolean benchIsVisible(HiddenColsAndStartState tstate) 
+    {
+    	return tstate.h.isVisible(tstate.hiddenColumn); 
+    }
+	
+	@Benchmark
+	@BenchmarkMode({Mode.Throughput})
+    public HiddenColumns benchReveal(HiddenColsAndStartState tstate) 
+    {
+		ColumnSelection sel = new ColumnSelection();
+    	tstate.h.revealHiddenColumns(tstate.hiddenColumn, sel);
+    	return tstate.h;
+    }
+	
+	@Benchmark
+	@BenchmarkMode({Mode.Throughput})
+    public HiddenColumns benchRevealAll(HiddenColsAndStartState tstate) 
+    {
+		ColumnSelection sel = new ColumnSelection();
+    	tstate.h.revealAllHiddenColumns(sel);
+    	return tstate.h;
+    }
+	
+	
 }
\ No newline at end of file
diff --git a/build.xml b/build.xml
index 89c3d24..d636a42 100755
--- a/build.xml
+++ b/build.xml
@@ -17,7 +17,9 @@
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
 -->
-<project name="jalviewX" default="usage" basedir=".">
+<project name="jalviewX" default="usage" basedir="."
+ xmlns:if="ant:if"
+    xmlns:unless="ant:unless">
   <target name="help" depends="usage" />
   <target name="usage" depends="init">
     <echo message="~~~Jalview Ant build.xml Usage~~~~" />
@@ -96,6 +98,10 @@
 
     <!-- default TestNG groups to run -->
     <property name="testng-groups" value="Functional" />
+    <!-- Java 9 JVM args -->
+    <condition property="java9">
+      <equals arg1="${ant.java.version}" arg2="9"/>
+    </condition>
 
     <!-- Don't change anything below here unless you know what you are doing! -->
     <!-- Url path for WebStart in JNLP file -->
@@ -298,6 +304,8 @@
         <pathelement location="${testOutputDir}" />
         <path refid="test.classpath" />
       </classpath>
+      <jvmarg value="--add-modules=java.se.ee" if:set="java9"/>
+      <jvmarg value="--illegal-access=warn" if:set="java9"/>
       <classfileset dir="${testOutputDir}" includes="**/*.class" />
     </testng>
   </target>
@@ -431,13 +439,14 @@
             <exclude name="jalview.jar" />
             <include name="*.jar" />
             <include name="*_*.jar" />
-            <exclude name="*jnilib.jar" />
+            <exclude name="*quaqua*.jar" />
           </fileset>
           <property name="jalview.version" value="${JALVIEW_VERSION}" />
         </resources>
         <resources os="Mac OS X">
           <fileset dir="${packageDir}">
-            <include name="*quaqua*.jnilib.jar" />
+          	 <include name="quaqua-filechooser-only-8.0.jar"/>
+            <include name="*quaqua64*.jnilib.jar" />
           </fileset>
         </resources>
 
@@ -580,7 +589,6 @@
 </target>
 
 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
-  <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
   <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
   <copy todir="${outputDir}/lang">
     <fileset dir="${resourceDir}/lang">
@@ -598,7 +606,6 @@
       <include name="MCview/**" />
       <include name="jalview/**" />
       <include name=".build_properties" />
-      <include name="images/idwidth.gif" />
       <include name="images/link.gif" />
       <include name="lang/**" />
     </fileset>
diff --git a/examples/testdata/4IM2_missing.pdb b/examples/testdata/4IM2_missing.pdb
new file mode 100644
index 0000000..35f94b2
--- /dev/null
+++ b/examples/testdata/4IM2_missing.pdb
@@ -0,0 +1,525 @@
+HEADER    TRANSFERASE/TRANSFERASE INHIBITOR       01-JAN-13   4IM2              
+TITLE     STRUCTURE OF TANK-BINDING KINASE 1  (Truncated test file)
+ATOM   3510  N   LEU A 468      76.337  90.332  -7.628  1.00168.53           N  
+ANISOU 3510  N   LEU A 468    19760  15191  29082   5189   1248  -1702       N  
+ATOM   3511  CA  LEU A 468      75.576  90.788  -6.476  1.00181.60           C  
+ANISOU 3511  CA  LEU A 468    21073  16927  30998   5158   1421  -2051       C  
+ATOM   3512  C   LEU A 468      76.285  91.971  -5.836  1.00196.57           C  
+ANISOU 3512  C   LEU A 468    23029  18636  33021   5053   1667  -2229       C  
+ATOM   3513  O   LEU A 468      75.727  93.067  -5.733  1.00197.97           O  
+ANISOU 3513  O   LEU A 468    23115  18581  33523   5166   1662  -2304       O  
+ATOM   3514  CB  LEU A 468      75.409  89.671  -5.449  1.00173.72           C  
+ANISOU 3514  CB  LEU A 468    19829  16340  29836   4981   1593  -2304       C  
+ATOM   3515  CG  LEU A 468      74.099  88.882  -5.420  1.00170.58           C  
+ANISOU 3515  CG  LEU A 468    19142  16142  29529   5074   1449  -2345       C  
+ATOM   3516  CD1 LEU A 468      74.023  87.940  -6.581  1.00167.98           C  
+ANISOU 3516  CD1 LEU A 468    18951  15858  29015   5180   1156  -2025       C  
+ATOM   3517  CD2 LEU A 468      73.988  88.096  -4.145  1.00165.16           C  
+ANISOU 3517  CD2 LEU A 468    18217  15818  28720   4865   1706  -2656       C  
+ATOM   3518  N   ASP A 469      77.529  91.753  -5.429  1.00208.80           N  
+ANISOU 3518  N   ASP A 469    24731  20282  34322   4836   1875  -2296       N  
+ATOM   3519  CA  ASP A 469      78.267  92.785  -4.720  1.00223.11           C  
+ANISOU 3519  CA  ASP A 469    26577  21960  36233   4701   2123  -2500       C  
+ATOM   3520  C   ASP A 469      78.653  93.973  -5.599  1.00231.96           C  
+ANISOU 3520  C   ASP A 469    27954  22654  37525   4817   2037  -2283       C  
+ATOM   3521  O   ASP A 469      78.718  95.100  -5.118  1.00235.71           O  
+ANISOU 3521  O   ASP A 469    28377  22940  38242   4798   2175  -2449       O  
+ATOM   3522  CB  ASP A 469      79.506  92.197  -4.057  1.00224.50           C  
+ANISOU 3522  CB  ASP A 469    26841  22370  36089   4433   2350  -2633       C  
+ATOM   3523  CG  ASP A 469      79.748  92.767  -2.679  1.00229.51           C  
+ANISOU 3523  CG  ASP A 469    27303  23107  36794   4254   2637  -3018       C  
+ATOM   3524  OD1 ASP A 469      79.958  93.992  -2.564  1.00232.36           O  
+ANISOU 3524  OD1 ASP A 469    27695  23203  37387   4262   2718  -3093       O  
+ATOM   3525  OD2 ASP A 469      79.751  91.979  -1.709  1.00229.48           O  
+ANISOU 3525  OD2 ASP A 469    27145  23450  36598   4098   2779  -3242       O  
+ATOM   3526  N   PHE A 470      78.904  93.735  -6.882  1.00233.88           N  
+ANISOU 3526  N   PHE A 470    28481  22742  37641   4931   1813  -1912       N  
+ATOM   3527  CA  PHE A 470      79.292  94.831  -7.766  1.00237.73           C  
+ANISOU 3527  CA  PHE A 470    29252  22819  38256   5033   1733  -1677       C  
+ATOM   3528  C   PHE A 470      78.103  95.470  -8.467  1.00232.15           C  
+ANISOU 3528  C   PHE A 470    28512  21868  37828   5322   1470  -1512       C  
+ATOM   3529  O   PHE A 470      78.021  96.691  -8.532  1.00230.69           O  
+ANISOU 3529  O   PHE A 470    28371  21372  37909   5402   1493  -1517       O  
+ATOM   3530  CB  PHE A 470      80.344  94.379  -8.784  1.00242.99           C  
+ANISOU 3530  CB  PHE A 470    30297  23410  38616   4976   1661  -1357       C  
+ATOM   3531  CG  PHE A 470      80.663  95.388  -9.839  1.00251.53           C  
+ANISOU 3531  CG  PHE A 470    31709  24074  39788   5089   1550  -1064       C  
+ATOM   3532  CD1 PHE A 470      81.658  96.315  -9.620  1.00252.90           C  
+ANISOU 3532  CD1 PHE A 470    32021  24036  40032   4942   1771  -1133       C  
+ATOM   3533  CD2 PHE A 470      80.005  95.389 -11.059  1.00255.02           C  
+ANISOU 3533  CD2 PHE A 470    32335  24339  40221   5330   1225   -715       C  
+ATOM   3534  CE1 PHE A 470      81.981  97.242 -10.575  1.00254.75           C  
+ANISOU 3534  CE1 PHE A 470    32569  23879  40344   5028   1688   -862       C  
+ATOM   3535  CE2 PHE A 470      80.321  96.320 -12.027  1.00256.76           C  
+ANISOU 3535  CE2 PHE A 470    32894  24173  40491   5427   1126   -433       C  
+ATOM   3536  CZ  PHE A 470      81.313  97.248 -11.784  1.00256.57           C  
+ANISOU 3536  CZ  PHE A 470    33006  23929  40550   5272   1365   -504       C  
+ATOM   3537  N   CYS A 471      77.190  94.665  -8.997  1.00176.88           N  
+ANISOU 3537  N   CYS A 471    20955  21812  24441   2225  -3821  -3711       N  
+ATOM   3538  CA  CYS A 471      76.124  95.233  -9.815  1.00176.41           C  
+ANISOU 3538  CA  CYS A 471    20820  21906  24301   2124  -3576  -3614       C  
+ATOM   3539  C   CYS A 471      74.868  95.631  -9.050  1.00176.82           C  
+ANISOU 3539  C   CYS A 471    21026  22206  23952   2247  -3588  -3734       C  
+ATOM   3540  O   CYS A 471      74.632  96.811  -8.854  1.00178.66           O  
+ANISOU 3540  O   CYS A 471    21175  22393  24314   2353  -3749  -3873       O  
+ATOM   3541  CB  CYS A 471      75.805  94.346 -11.019  1.00173.95           C  
+ANISOU 3541  CB  CYS A 471    20521  21694  23877   1925  -3217  -3359       C  
+ATOM   3542  SG  CYS A 471      76.954  94.571 -12.398  1.00273.04           S  
+ANISOU 3542  SG  CYS A 471    32850  33934  36957   1863  -3075  -3146       S  
+ATOM   3543  N   ILE A 472      74.068  94.670  -8.603  1.00173.50           N  
+ANISOU 3543  N   ILE A 472    20813  22023  23085   2253  -3402  -3662       N  
+ATOM   3544  CA  ILE A 472      72.771  95.033  -8.022  1.00171.09           C  
+ANISOU 3544  CA  ILE A 472    20616  21936  22453   2374  -3307  -3694       C  
+ATOM   3545  C   ILE A 472      72.832  96.022  -6.874  1.00177.82           C  
+ANISOU 3545  C   ILE A 472    21591  22750  23222   2698  -3611  -3931       C  
+ATOM   3546  O   ILE A 472      71.992  96.914  -6.776  1.00182.92           O  
+ANISOU 3546  O   ILE A 472    22220  23491  23792   2778  -3598  -3985       O  
+ATOM   3547  CB  ILE A 472      71.979  93.843  -7.518  1.00159.41           C  
+ANISOU 3547  CB  ILE A 472    19318  20653  20599   2393  -3038  -3546       C  
+ATOM   3548  CG1 ILE A 472      70.708  93.667  -8.341  1.00147.27           C  
+ANISOU 3548  CG1 ILE A 472    17653  19253  19051   2196  -2745  -3384       C  
+ATOM   3549  CG2 ILE A 472      71.526  94.090  -6.105  1.00155.95           C  
+ANISOU 3549  CG2 ILE A 472    19129  20312  19812   2752  -3085  -3637       C  
+ATOM   3550  CD1 ILE A 472      70.927  92.915  -9.606  1.00135.92           C  
+ANISOU 3550  CD1 ILE A 472    16097  17752  17794   1929  -2643  -3254       C  
+ATOM   3551  N   ARG A 473      73.812  95.865  -5.996  1.00180.33           N  
+ANISOU 3551  N   ARG A 473    22055  22917  23544   2920  -3920  -4092       N  
+ATOM   3552  CA  ARG A 473      73.860  96.762  -4.877  1.00189.65           C  
+ANISOU 3552  CA  ARG A 473    23415  24034  24610   3307  -4283  -4357       C  
+ATOM   3553  C   ARG A 473      74.328  98.021  -5.558  1.00185.98           C  
+ANISOU 3553  C   ARG A 473    22628  23344  24692   3195  -4530  -4477       C  
+ATOM   3554  O   ARG A 473      73.519  98.885  -5.866  1.00181.76           O  
+ANISOU 3554  O   ARG A 473    22002  22904  24153   3165  -4446  -4474       O  
+ATOM   3555  CB  ARG A 473      74.803  96.287  -3.768  1.00205.24           C  
+ANISOU 3555  CB  ARG A 473    25661  25862  26460   3635  -4629  -4545       C  
+ATOM   3556  CG  ARG A 473      74.468  96.921  -2.433  1.00220.50           C  
+ANISOU 3556  CG  ARG A 473    27955  27814  28011   4171  -4923  -4787       C  
+ATOM   3557  CD  ARG A 473      75.337  96.433  -1.295  1.00232.58           C  
+ANISOU 3557  CD  ARG A 473    29837  29192  29341   4591  -5300  -5003       C  
+ATOM   3558  NE  ARG A 473      76.763  96.602  -1.549  1.00237.46           N  
+ANISOU 3558  NE  ARG A 473    30220  29440  30564   4489  -5773  -5205       N  
+ATOM   3559  CZ  ARG A 473      77.716  95.991  -0.861  1.00240.32           C  
+ANISOU 3559  CZ  ARG A 473    30786  29623  30903   4725  -6098  -5371       C  
+ATOM   3560  NH1 ARG A 473      77.388  95.172   0.115  1.00241.12           N  
+ANISOU 3560  NH1 ARG A 473    31370  29900  30344   5100  -5978  -5355       N  
+ATOM   3561  NH2 ARG A 473      78.988  96.195  -1.159  1.00241.54           N  
+ANISOU 3561  NH2 ARG A 473    30651  29398  31724   4605  -6518  -5533       N  
+ATOM   3562  N   ASN A 474      75.608  98.073  -5.901  1.00188.74           N  
+ANISOU 3562  N   ASN A 474    22768  23381  25563   3107  -4772  -4534       N  
+ATOM   3563  CA  ASN A 474      76.168  99.264  -6.526  1.00188.61           C  
+ANISOU 3563  CA  ASN A 474    22395  23075  26194   3026  -4977  -4605       C  
+ATOM   3564  C   ASN A 474      75.420  99.892  -7.729  1.00173.98           C  
+ANISOU 3564  C   ASN A 474    20312  21326  24467   2781  -4623  -4414       C  
+ATOM   3565  O   ASN A 474      75.482 101.107  -7.891  1.00176.08           O  
+ANISOU 3565  O   ASN A 474    20374  21426  25104   2827  -4803  -4518       O  
+ATOM   3566  CB  ASN A 474      77.650  99.066  -6.857  1.00199.45           C  
+ANISOU 3566  CB  ASN A 474    23514  24060  28207   2939  -5170  -4595       C  
+ATOM   3567  CG  ASN A 474      78.504  98.809  -5.625  1.00210.23           C  
+ANISOU 3567  CG  ASN A 474    25062  25219  29597   3243  -5689  -4883       C  
+ATOM   3568  OD1 ASN A 474      78.174  99.240  -4.527  1.00215.26           O  
+ANISOU 3568  OD1 ASN A 474    25969  25891  29928   3596  -6043  -5160       O  
+ATOM   3569  ND2 ASN A 474      79.613  98.103  -5.810  1.00212.07           N  
+ANISOU 3569  ND2 ASN A 474    25176  25222  30179   3148  -5748  -4822       N  
+ATOM   3570  N   ILE A 475      74.722  99.114  -8.562  1.00161.86           N  
+ANISOU 3570  N   ILE A 475    18813  20033  22652   2556  -4165  -4158       N  
+ATOM   3571  CA  ILE A 475      74.022  99.727  -9.709  1.00154.84           C  
+ANISOU 3571  CA  ILE A 475    17755  19216  21861   2390  -3885  -4015       C  
+ATOM   3572  C   ILE A 475      72.785 100.520  -9.312  1.00159.27           C  
+ANISOU 3572  C   ILE A 475    18401  19995  22121   2490  -3891  -4125       C  
+ATOM   3573  O   ILE A 475      72.662 101.687  -9.663  1.00162.60           O  
+ANISOU 3573  O   ILE A 475    18651  20327  22804   2505  -3962  -4186       O  
+ATOM   3574  CB  ILE A 475      73.600  98.727 -10.818  1.00214.93           C  
+ANISOU 3574  CB  ILE A 475    25397  26975  29293   2173  -3475  -3753       C  
+ATOM   3575  CG1 ILE A 475      74.808  98.227 -11.613  1.00218.74           C  
+ANISOU 3575  CG1 ILE A 475    25753  27211  30145   2083  -3390  -3585       C  
+ATOM   3576  CG2 ILE A 475      72.618  99.379 -11.789  1.00210.37           C  
+ANISOU 3576  CG2 ILE A 475    24743  26509  28681   2097  -3256  -3677       C  
+ATOM   3577  CD1 ILE A 475      74.446  97.201 -12.664  1.00218.15           C  
+ANISOU 3577  CD1 ILE A 475    25777  27260  29850   1946  -3056  -3359       C  
+ATOM   3578  N   GLU A 476      71.856  99.893  -8.600  1.00156.45           N  
+ANISOU 3578  N   GLU A 476    18293  19907  21245   2571  -3778  -4120       N  
+ATOM   3579  CA  GLU A 476      70.623 100.594  -8.252  1.00142.72           C  
+ANISOU 3579  CA  GLU A 476    16627  18370  19231   2677  -3720  -4176       C  
+ATOM   3580  C   GLU A 476      70.845 101.560  -7.094  1.00144.41           C  
+ANISOU 3580  C   GLU A 476    16959  18500  19412   3012  -4114  -4440       C  
+ATOM   3581  O   GLU A 476      70.012 102.417  -6.811  1.00142.58           O  
+ANISOU 3581  O   GLU A 476    16768  18380  19024   3141  -4136  -4517       O  
+ATOM   3582  CB  GLU A 476      69.486  99.616  -7.958  1.00128.68           C  
+ANISOU 3582  CB  GLU A 476    15020  16860  17012   2665  -3395  -4018       C  
+ATOM   3583  CG  GLU A 476      69.562  98.905  -6.628  1.00128.73           C  
+ANISOU 3583  CG  GLU A 476    15321  16930  16662   2941  -3433  -4041       C  
+ATOM   3584  CD  GLU A 476      68.465  97.866  -6.484  1.00133.35           C  
+ANISOU 3584  CD  GLU A 476    15992  17719  16955   2900  -3026  -3806       C  
+ATOM   3585  OE1 GLU A 476      68.285  97.061  -7.422  1.00132.30           O  
+ANISOU 3585  OE1 GLU A 476    15710  17598  16962   2603  -2816  -3643       O  
+ATOM   3586  OE2 GLU A 476      67.768  97.860  -5.448  1.00136.37           O  
+ANISOU 3586  OE2 GLU A 476    16588  18223  17003   3196  -2912  -3773       O  
+ATOM   3587  N   LYS A 477      71.990 101.424  -6.439  1.00148.46           N  
+ANISOU 3587  N   LYS A 477    17534  18788  20087   3179  -4467  -4596       N  
+ATOM   3588  CA  LYS A 477      72.399 102.365  -5.405  1.00154.25           C  
+ANISOU 3588  CA  LYS A 477    18378  19348  20882   3544  -4976  -4907       C  
+ATOM   3589  C   LYS A 477      72.634 103.732  -5.994  1.00159.76           C  
+ANISOU 3589  C   LYS A 477    18754  19833  22117   3467  -5183  -5014       C  
+ATOM   3590  O   LYS A 477      72.568 104.742  -5.292  1.00158.01           O  
+ANISOU 3590  O   LYS A 477    18598  19516  21921   3749  -5568  -5266       O  
+ATOM   3591  CB  LYS A 477      73.667 101.883  -4.706  1.00154.03           C  
+ANISOU 3591  CB  LYS A 477    18446  19057  21022   3730  -5372  -5076       C  
+ATOM   3592  CG  LYS A 477      73.367 100.787  -3.750  1.00149.76           C  
+ANISOU 3592  CG  LYS A 477    18324  18717  19861   3975  -5258  -5042       C  
+ATOM   3593  CD  LYS A 477      74.437 100.554  -2.740  1.00143.39           C  
+ANISOU 3593  CD  LYS A 477    17737  17664  19082   4327  -5762  -5306       C  
+ATOM   3594  CE  LYS A 477      73.739 100.087  -1.488  1.00145.72           C  
+ANISOU 3594  CE  LYS A 477    18569  18186  18613   4805  -5697  -5337       C  
+ATOM   3595  NZ  LYS A 477      74.661  99.556  -0.469  1.00149.42           N  
+ANISOU 3595  NZ  LYS A 477    19366  18470  18936   5206  -6108  -5561       N  
+ATOM   3596  N   THR A 478      72.908 103.757  -7.293  1.00166.45           N  
+ANISOU 3596  N   THR A 478    19271  20589  23384   3124  -4918  -4810       N  
+ATOM   3597  CA  THR A 478      73.186 105.012  -7.968  1.00170.99           C  
+ANISOU 3597  CA  THR A 478    19509  20929  24531   3052  -5023  -4844       C  
+ATOM   3598  C   THR A 478      71.905 105.733  -8.391  1.00172.33           C  
+ANISOU 3598  C   THR A 478    19686  21358  24435   2999  -4780  -4796       C  
+ATOM   3599  O   THR A 478      71.021 105.170  -9.046  1.00163.10           O  
+ANISOU 3599  O   THR A 478    18581  20461  22928   2823  -4356  -4594       O  
+ATOM   3600  CB  THR A 478      74.217 104.856  -9.128  1.00146.93           C  
+ANISOU 3600  CB  THR A 478    16115  17589  22125   2815  -4843  -4626       C  
+ATOM   3601  OG1 THR A 478      74.873 106.106  -9.369  1.00147.15           O  
+ANISOU 3601  OG1 THR A 478    15790  17239  22881   2857  -5085  -4705       O  
+ATOM   3602  CG2 THR A 478      73.562 104.391 -10.425  1.00144.32           C  
+ANISOU 3602  CG2 THR A 478    15764  17473  21597   2570  -4282  -4318       C  
+ATOM   3603  N   VAL A 479      71.809 106.979  -7.944  1.00177.73           N  
+ANISOU 3603  N   VAL A 479    20309  21929  25291   3181  -5110  -5014       N  
+ATOM   3604  CA  VAL A 479      70.674 107.838  -8.218  1.00175.65           C  
+ANISOU 3604  CA  VAL A 479    20044  21875  24819   3171  -4959  -5013       C  
+ATOM   3605  C   VAL A 479      71.176 109.077  -8.939  1.00177.67           C  
+ANISOU 3605  C   VAL A 479    19928  21830  25749   3101  -5069  -5035       C  
+ATOM   3606  O   VAL A 479      72.353 109.417  -8.840  1.00179.02           O  
+ANISOU 3606  O   VAL A 479    19865  21600  26555   3150  -5387  -5121       O  
+ATOM   3607  CB  VAL A 479      69.983 108.266  -6.909  1.00168.37           C  
+ANISOU 3607  CB  VAL A 479    19442  21113  23418   3524  -5243  -5249       C  
+ATOM   3608  CG1 VAL A 479      69.008 109.403  -7.169  1.00162.23           C  
+ANISOU 3608  CG1 VAL A 479    18603  20470  22565   3531  -5176  -5285       C  
+ATOM   3609  CG2 VAL A 479      69.288 107.080  -6.256  1.00163.89           C  
+ANISOU 3609  CG2 VAL A 479    19236  20856  22180   3624  -4991  -5142       C  
+ATOM   3610  N   MET A 486      57.931 103.433  -6.150  1.00 92.00           N  
+ANISOU 3610  N   MET A 486    10154  13425  11375   3371  -1523  -3283       N  
+ATOM   3611  CA  MET A 486      56.824 104.104  -5.482  1.00110.61           C  
+ANISOU 3611  CA  MET A 486    12558  15882  13585   3644  -1287  -3161       C  
+ATOM   3612  C   MET A 486      56.182 105.150  -6.389  1.00111.38           C  
+ANISOU 3612  C   MET A 486    12428  16016  13877   3424  -1416  -3308       C  
+ATOM   3613  O   MET A 486      56.000 106.305  -6.002  1.00120.35           O  
+ANISOU 3613  O   MET A 486    13691  17243  14794   3639  -1526  -3430       O  
+ATOM   3614  CB  MET A 486      57.288 104.743  -4.170  1.00120.60           C  
+ANISOU 3614  CB  MET A 486    14253  17221  14347   4174  -1395  -3243       C  
+ATOM   3615  CG  MET A 486      58.405 105.768  -4.316  1.00126.87           C  
+ANISOU 3615  CG  MET A 486    15171  17987  15047   4196  -1944  -3629       C  
+ATOM   3616  SD  MET A 486      58.150 107.169  -3.210  1.00146.78           S  
+ANISOU 3616  SD  MET A 486    18044  20597  17128   4757  -2124  -3782       S  
+ATOM   3617  CE  MET A 486      58.003 106.326  -1.640  1.00102.35           C  
+ANISOU 3617  CE  MET A 486    12883  15002  11003   5391  -1797  -3524       C  
+ATOM   3618  N   GLY A 496      57.154  99.412  -2.065  1.00157.62           N  
+ANISOU 3618  N   GLY A 496    19150  21656  19083   4616     82  -2024       N  
+ATOM   3619  CA  GLY A 496      57.031  99.217  -3.498  1.00158.07           C  
+ANISOU 3619  CA  GLY A 496    18749  21636  19677   3991   -116  -2141       C  
+ATOM   3620  C   GLY A 496      57.664  97.914  -3.942  1.00163.71           C  
+ANISOU 3620  C   GLY A 496    19349  22235  20619   3709   -140  -2093       C  
+ATOM   3621  O   GLY A 496      58.040  97.090  -3.111  1.00167.17           O  
+ANISOU 3621  O   GLY A 496    20009  22652  20858   3970     79  -1915       O  
+ATOM   3622  N   GLU A 497      57.778  97.722  -5.254  1.00166.67           N  
+ANISOU 3622  N   GLU A 497    19413  22530  21383   3222   -403  -2250       N  
+ATOM   3623  CA  GLU A 497      58.431  96.534  -5.792  1.00170.73           C  
+ANISOU 3623  CA  GLU A 497    19840  22933  22098   2955   -485  -2239       C  
+ATOM   3624  C   GLU A 497      59.931  96.621  -5.556  1.00172.64           C  
+ANISOU 3624  C   GLU A 497    20403  23228  21965   3043   -809  -2472       C  
+ATOM   3625  O   GLU A 497      60.589  95.609  -5.311  1.00173.01           O  
+ANISOU 3625  O   GLU A 497    20547  23223  21965   3047   -764  -2395       O  
+ATOM   3626  CB  GLU A 497      58.173  96.394  -7.290  1.00169.62           C  
+ANISOU 3626  CB  GLU A 497    19361  22681  22408   2505   -727  -2374       C  
+ATOM   3627  CG  GLU A 497      56.882  97.012  -7.777  1.00173.11           C  
+ANISOU 3627  CG  GLU A 497    19518  23086  23171   2413   -663  -2350       C  
+ATOM   3628  CD  GLU A 497      56.703  96.840  -9.270  1.00173.61           C  
+ANISOU 3628  CD  GLU A 497    19329  23013  23621   2054   -974  -2531       C  
+ATOM   3629  OE1 GLU A 497      57.597  96.241  -9.908  1.00170.78           O  
+ANISOU 3629  OE1 GLU A 497    19040  22600  23250   1901  -1202  -2647       O  
+ATOM   3630  OE2 GLU A 497      55.672  97.300  -9.805  1.00174.73           O  
+ANISOU 3630  OE2 GLU A 497    19233  23093  24064   1967   -999  -2559       O  
+ATOM   3631  N   ILE A 498      60.466  97.836  -5.652  1.00171.44           N  
+ANISOU 3631  N   ILE A 498    20381  23149  21608   3107  -1147  -2757       N  
+ATOM   3632  CA  ILE A 498      61.883  98.078  -5.403  1.00167.93           C  
+ANISOU 3632  CA  ILE A 498    20186  22695  20926   3210  -1503  -2995       C  
+ATOM   3633  C   ILE A 498      62.251  97.620  -4.004  1.00173.82           C  
+ANISOU 3633  C   ILE A 498    21298  23465  21280   3659  -1379  -2903       C  
+ATOM   3634  O   ILE A 498      63.315  97.034  -3.789  1.00168.12           O  
+ANISOU 3634  O   ILE A 498    20732  22684  20462   3692  -1544  -2980       O  
+ATOM   3635  CB  ILE A 498      62.227  99.564  -5.520  1.00165.53           C  
+ANISOU 3635  CB  ILE A 498    19934  22420  20540   3287  -1855  -3283       C  
+ATOM   3636  CG1 ILE A 498      61.848 100.100  -6.901  1.00171.37           C  
+ANISOU 3636  CG1 ILE A 498    20360  23137  21618   2911  -1947  -3365       C  
+ATOM   3637  CG2 ILE A 498      63.706  99.798  -5.239  1.00153.61           C  
+ANISOU 3637  CG2 ILE A 498    18613  20820  18931   3398  -2256  -3525       C  
+ATOM   3638  CD1 ILE A 498      61.891 101.605  -6.996  1.00174.73           C  
+ANISOU 3638  CD1 ILE A 498    20793  23594  22004   2996  -2195  -3587       C  
+ATOM   3639  N   SER A 499      61.362  97.890  -3.054  1.00187.32           N  
+ANISOU 3639  N   SER A 499    23169  25252  22753   4049  -1074  -2727       N  
+ATOM   3640  CA  SER A 499      61.558  97.444  -1.683  1.00198.47           C  
+ANISOU 3640  CA  SER A 499    24999  26682  23729   4594   -880  -2593       C  
+ATOM   3641  C   SER A 499      61.611  95.926  -1.651  1.00206.95           C  
+ANISOU 3641  C   SER A 499    26003  27687  24943   4481   -548  -2315       C  
+ATOM   3642  O   SER A 499      62.302  95.334  -0.823  1.00211.11           O  
+ANISOU 3642  O   SER A 499    26867  28195  25151   4806   -533  -2293       O  
+ATOM   3643  CB  SER A 499      60.435  97.952  -0.780  1.00200.16           C  
+ANISOU 3643  CB  SER A 499    25385  26976  23690   5064   -498  -2368       C  
+ATOM   3644  OG  SER A 499      60.635  97.541   0.556  1.00203.12           O  
+ANISOU 3644  OG  SER A 499    26244  27359  23574   5697   -286  -2224       O  
+ATOM   3645  N   ASP A 500      60.877  95.300  -2.564  1.00209.43           N  
+ANISOU 3645  N   ASP A 500    25883  27938  25751   4040   -320  -2123       N  
+ATOM   3646  CA  ASP A 500      60.862  93.851  -2.655  1.00212.36           C  
+ANISOU 3646  CA  ASP A 500    26120  28207  26361   3883    -39  -1865       C  
+ATOM   3647  C   ASP A 500      62.097  93.307  -3.366  1.00203.21           C  
+ANISOU 3647  C   ASP A 500    24946  26999  25265   3557   -426  -2093       C  
+ATOM   3648  O   ASP A 500      62.511  92.195  -3.092  1.00204.96           O  
+ANISOU 3648  O   ASP A 500    25238  27165  25472   3573   -286  -1954       O  
+ATOM   3649  CB  ASP A 500      59.580  93.355  -3.335  1.00221.23           C  
+ANISOU 3649  CB  ASP A 500    26765  29217  28075   3573    287  -1593       C  
+ATOM   3650  CG  ASP A 500      58.346  93.583  -2.486  1.00233.55           C  
+ANISOU 3650  CG  ASP A 500    28310  30773  29657   3938    816  -1243       C  
+ATOM   3651  OD1 ASP A 500      58.502  93.807  -1.272  1.00239.09           O  
+ANISOU 3651  OD1 ASP A 500    29432  31558  29852   4492   1029  -1137       O  
+ATOM   3652  OD2 ASP A 500      57.226  93.532  -3.034  1.00237.24           O  
+ANISOU 3652  OD2 ASP A 500    28355  31128  30656   3709   1011  -1072       O  
+ATOM   3653  N   ILE A 501      62.692  94.094  -4.258  1.00192.67           N  
+ANISOU 3653  N   ILE A 501    23525  25673  24008   3292   -875  -2413       N  
+ATOM   3654  CA  ILE A 501      63.864  93.633  -5.007  1.00181.71           C  
+ANISOU 3654  CA  ILE A 501    22108  24215  22719   3006  -1195  -2587       C  
+ATOM   3655  C   ILE A 501      65.165  93.699  -4.196  1.00170.68           C  
+ANISOU 3655  C   ILE A 501    21064  22814  20972   3287  -1450  -2764       C  
+ATOM   3656  O   ILE A 501      65.940  92.735  -4.173  1.00164.70           O  
+ANISOU 3656  O   ILE A 501    20376  21999  20202   3222  -1476  -2736       O  
+ATOM   3657  CB  ILE A 501      64.023  94.385  -6.353  1.00138.03           C  
+ANISOU 3657  CB  ILE A 501    16341  18649  17453   2657  -1507  -2802       C  
+ATOM   3658  CG1 ILE A 501      63.385  93.589  -7.491  1.00130.33           C  
+ANISOU 3658  CG1 ILE A 501    15061  17587  16872   2296  -1411  -2683       C  
+ATOM   3659  CG2 ILE A 501      65.491  94.642  -6.682  1.00137.98           C  
+ANISOU 3659  CG2 ILE A 501    16437  18581  17410   2596  -1883  -3037       C  
+ATOM   3660  CD1 ILE A 501      61.877  93.516  -7.426  1.00127.50           C  
+ANISOU 3660  CD1 ILE A 501    14480  17217  16748   2292  -1111  -2482       C  
+ATOM   3661  N   HIS A 502      65.396  94.829  -3.532  1.00164.00           N  
+ANISOU 3661  N   HIS A 502    20439  22007  19869   3613  -1676  -2964       N  
+ATOM   3662  CA  HIS A 502      66.603  95.022  -2.737  1.00157.69           C  
+ANISOU 3662  CA  HIS A 502    19968  21147  18800   3931  -2029  -3195       C  
+ATOM   3663  C   HIS A 502      66.627  94.018  -1.594  1.00162.64           C  
+ANISOU 3663  C   HIS A 502    20933  21795  19069   4322  -1761  -3012       C  
+ATOM   3664  O   HIS A 502      67.677  93.496  -1.229  1.00164.35           O  
+ANISOU 3664  O   HIS A 502    21348  21935  19163   4433  -1971  -3125       O  
+ATOM   3665  CB  HIS A 502      66.654  96.452  -2.195  1.00150.83           C  
+ANISOU 3665  CB  HIS A 502    19272  20282  17755   4264  -2351  -3452       C  
+ATOM   3666  CG  HIS A 502      67.989  97.117  -2.348  1.00143.78           C  
+ANISOU 3666  CG  HIS A 502    18387  19223  17019   4248  -2929  -3804       C  
+ATOM   3667  ND1 HIS A 502      68.672  97.155  -3.544  1.00137.00           N  
+ANISOU 3667  ND1 HIS A 502    17193  18253  16609   3785  -3096  -3872       N  
+ATOM   3668  CD2 HIS A 502      68.759  97.787  -1.457  1.00140.15           C  
+ANISOU 3668  CD2 HIS A 502    18217  18647  16387   4674  -3387  -4099       C  
+ATOM   3669  CE1 HIS A 502      69.807  97.814  -3.383  1.00131.33           C  
+ANISOU 3669  CE1 HIS A 502    16503  17343  16055   3893  -3583  -4155       C  
+ATOM   3670  NE2 HIS A 502      69.883  98.208  -2.125  1.00130.34           N  
+ANISOU 3670  NE2 HIS A 502    16741  17200  15583   4416  -3815  -4326       N  
+ATOM   3671  N   THR A 503      65.450  93.751  -1.039  1.00163.37           N  
+ANISOU 3671  N   THR A 503    21080  21971  19022   4552  -1268  -2705       N  
+ATOM   3672  CA  THR A 503      65.295  92.771   0.033  1.00163.31           C  
+ANISOU 3672  CA  THR A 503    21384  21972  18696   4974   -872  -2437       C  
+ATOM   3673  C   THR A 503      65.393  91.327  -0.475  1.00151.49           C  
+ANISOU 3673  C   THR A 503    19659  20415  17484   4610   -614  -2206       C  
+ATOM   3674  O   THR A 503      65.955  90.464   0.198  1.00146.11           O  
+ANISOU 3674  O   THR A 503    19247  19705  16563   4853   -520  -2130       O  
+ATOM   3675  CB  THR A 503      63.956  92.972   0.783  1.00170.09           C  
+ANISOU 3675  CB  THR A 503    22342  22899  19387   5379   -334  -2106       C  
+ATOM   3676  OG1 THR A 503      64.026  94.162   1.576  1.00176.61           O  
+ANISOU 3676  OG1 THR A 503    23551  23775  19778   5902   -585  -2325       O  
+ATOM   3677  CG2 THR A 503      63.645  91.790   1.693  1.00171.53           C  
+ANISOU 3677  CG2 THR A 503    22747  23054  19374   5760    235  -1707       C  
+ATOM   3678  N   LYS A 504      64.865  91.071  -1.669  1.00141.41           N  
+ANISOU 3678  N   LYS A 504    17911  19106  16711   4058   -541  -2117       N  
+ATOM   3679  CA  LYS A 504      64.918  89.730  -2.251  1.00138.96           C  
+ANISOU 3679  CA  LYS A 504    17368  18711  16719   3706   -369  -1930       C  
+ATOM   3680  C   LYS A 504      66.335  89.382  -2.646  1.00142.04           C  
+ANISOU 3680  C   LYS A 504    17848  19062  17058   3520   -779  -2178       C  
+ATOM   3681  O   LYS A 504      66.762  88.230  -2.559  1.00134.46           O  
+ANISOU 3681  O   LYS A 504    16927  18053  16108   3463   -666  -2057       O  
+ATOM   3682  CB  LYS A 504      64.010  89.614  -3.477  1.00129.82           C  
+ANISOU 3682  CB  LYS A 504    15721  17488  16116   3223   -303  -1839       C  
+ATOM   3683  CG  LYS A 504      62.585  89.222  -3.164  1.00130.75           C  
+ANISOU 3683  CG  LYS A 504    15616  17544  16518   3307    225  -1458       C  
+ATOM   3684  N   LEU A 505      67.053  90.395  -3.100  1.00138.41           N  
+ANISOU 3684  N   LEU A 505    17394  18602  16593   3427  -1237  -2505       N  
+ATOM   3685  CA  LEU A 505      68.435  90.224  -3.458  1.00120.29           C  
+ANISOU 3685  CA  LEU A 505    15154  16230  14322   3285  -1619  -2726       C  
+ATOM   3686  C   LEU A 505      69.260  89.889  -2.223  1.00124.70           C  
+ANISOU 3686  C   LEU A 505    16126  16770  14484   3724  -1710  -2800       C  
+ATOM   3687  O   LEU A 505      70.166  89.052  -2.259  1.00124.02           O  
+ANISOU 3687  O   LEU A 505    16106  16619  14396   3643  -1808  -2823       O  
+ATOM   3688  CB  LEU A 505      68.966  91.499  -4.066  1.00109.42           C  
+ANISOU 3688  CB  LEU A 505    13673  14807  13094   3171  -2036  -3016       C  
+ATOM   3689  CG  LEU A 505      70.386  91.097  -4.404  1.00128.61           C  
+ANISOU 3689  CG  LEU A 505    16120  17111  15635   3034  -2336  -3157       C  
+ATOM   3690  CD1 LEU A 505      70.509  91.048  -5.920  1.00141.22           C  
+ANISOU 3690  CD1 LEU A 505    17393  18648  17616   2580  -2370  -3131       C  
+ATOM   3691  CD2 LEU A 505      71.441  91.946  -3.655  1.00114.58           C  
+ANISOU 3691  CD2 LEU A 505    14554  15224  13758   3350  -2784  -3462       C  
+ATOM   3692  N   LEU A 506      68.951  90.579  -1.132  1.00130.40           N  
+ANISOU 3692  N   LEU A 506    17159  17539  14847   4233  -1705  -2854       N  
+ATOM   3693  CA  LEU A 506      69.612  90.336   0.139  1.00131.63           C  
+ANISOU 3693  CA  LEU A 506    17798  17665  14549   4786  -1814  -2947       C  
+ATOM   3694  C   LEU A 506      69.501  88.865   0.507  1.00144.65           C  
+ANISOU 3694  C   LEU A 506    19548  19330  16080   4841  -1380  -2638       C  
+ATOM   3695  O   LEU A 506      70.448  88.287   1.024  1.00156.36           O  
+ANISOU 3695  O   LEU A 506    21304  20754  17351   5038  -1550  -2741       O  
+ATOM   3696  CB  LEU A 506      69.008  91.206   1.240  1.00120.17           C  
+ANISOU 3696  CB  LEU A 506    16713  16270  12675   5409  -1772  -2980       C  
+ATOM   3697  N   ARG A 507      68.351  88.260   0.214  1.00146.01           N  
+ANISOU 3697  N   ARG A 507    19470  19552  16453   4658   -839  -2263       N  
+ATOM   3698  CA  ARG A 507      68.159  86.831   0.443  1.00152.26           C  
+ANISOU 3698  CA  ARG A 507    20261  20320  17271   4649   -394  -1930       C  
+ATOM   3699  C   ARG A 507      69.164  86.004  -0.360  1.00145.14           C  
+ANISOU 3699  C   ARG A 507    19199  19352  16597   4200   -653  -2042       C  
+ATOM   3700  O   ARG A 507      69.471  84.873   0.007  1.00142.95           O  
+ANISOU 3700  O   ARG A 507    19044  19045  16224   4273   -450  -1882       O  
+ATOM   3701  CB  ARG A 507      66.724  86.401   0.111  1.00161.16           C  
+ANISOU 3701  CB  ARG A 507    21023  21434  18777   4463    165  -1523       C  
+ATOM   3702  CG  ARG A 507      65.661  86.975   1.046  1.00177.63           C  
+ANISOU 3702  CG  ARG A 507    23283  23565  20645   4978    585  -1290       C  
+ATOM   3703  CD  ARG A 507      64.263  86.468   0.696  1.00187.68           C  
+ANISOU 3703  CD  ARG A 507    24111  24757  22442   4769   1148   -857       C  
+ATOM   3704  NE  ARG A 507      63.229  87.082   1.527  1.00198.88           N  
+ANISOU 3704  NE  ARG A 507    25661  26202  23704   5259   1588   -600       N  
+ATOM   3705  CZ  ARG A 507      61.923  86.883   1.368  1.00205.71           C  
+ANISOU 3705  CZ  ARG A 507    26137  26967  25058   5169   2095   -210       C  
+ATOM   3706  NH1 ARG A 507      61.484  86.084   0.406  1.00207.33           N  
+ANISOU 3706  NH1 ARG A 507    25797  27020  25959   4610   2159    -75       N  
+ATOM   3707  NH2 ARG A 507      61.055  87.485   2.171  1.00208.11           N  
+ANISOU 3707  NH2 ARG A 507    26596  27293  25185   5668   2517     41       N  
+ATOM   3708  N   LEU A 508      69.681  86.579  -1.445  1.00134.19           N  
+ANISOU 3708  N   LEU A 508    17555  17933  15496   3776  -1072  -2294       N  
+ATOM   3709  CA  LEU A 508      70.654  85.888  -2.287  1.00125.06           C  
+ANISOU 3709  CA  LEU A 508    16259  16704  14555   3385  -1304  -2382       C  
+ATOM   3710  C   LEU A 508      72.070  85.983  -1.730  1.00133.75           C  
+ANISOU 3710  C   LEU A 508    17660  17739  15419   3609  -1705  -2655       C  
+ATOM   3711  O   LEU A 508      72.775  84.975  -1.650  1.00132.42           O  
+ANISOU 3711  O   LEU A 508    17581  17530  15202   3562  -1700  -2615       O  
+ATOM   3712  CB  LEU A 508      70.606  86.404  -3.726  1.00112.64           C  
+ANISOU 3712  CB  LEU A 508    14312  15095  13392   2907  -1513  -2482       C  
+ATOM   3713  CG  LEU A 508      69.271  86.186  -4.436  1.00113.17           C  
+ANISOU 3713  CG  LEU A 508    14056  15174  13769   2653  -1215  -2260       C  
+ATOM   3714  CD1 LEU A 508      69.459  86.184  -5.945  1.00106.22           C  
+ANISOU 3714  CD1 LEU A 508    12898  14225  13237   2216  -1432  -2343       C  
+ATOM   3715  CD2 LEU A 508      68.613  84.894  -3.968  1.00117.32           C  
+ANISOU 3715  CD2 LEU A 508    14560  15678  14341   2703   -779  -1932       C  
+ATOM   3716  N   SER A 509      72.491  87.188  -1.355  1.00130.72           N  
+ANISOU 3716  N   SER A 509    17414  17317  14936   3856  -2085  -2944       N  
+ATOM   3717  CA  SER A 509      73.767  87.347  -0.663  1.00136.66           C  
+ANISOU 3717  CA  SER A 509    18457  17948  15519   4156  -2531  -3236       C  
+ATOM   3718  C   SER A 509      73.698  86.583   0.646  1.00143.40           C  
+ANISOU 3718  C   SER A 509    19773  18845  15866   4687  -2319  -3138       C  
+ATOM   3719  O   SER A 509      74.680  85.977   1.082  1.00138.35           O  
+ANISOU 3719  O   SER A 509    19358  18121  15090   4839  -2521  -3256       O  
+ATOM   3720  CB  SER A 509      74.089  88.820  -0.410  1.00130.15           C  
+ANISOU 3720  CB  SER A 509    17685  17028  14738   4382  -3008  -3572       C  
+ATOM   3721  OG  SER A 509      74.991  89.319  -1.384  1.00125.27           O  
+ANISOU 3721  OG  SER A 509    16739  16248  14609   4003  -3376  -3749       O  
+ATOM   3722  N   SER A 510      72.520  86.615   1.263  1.00144.65           N  
+ANISOU 3722  N   SER A 510    20078  19123  15761   4999  -1878  -2899       N  
+ATOM   3723  CA  SER A 510      72.236  85.777   2.417  1.00148.97           C  
+ANISOU 3723  CA  SER A 510    21044  19713  15846   5526  -1487  -2677       C  
+ATOM   3724  C   SER A 510      72.424  84.315   2.046  1.00145.48           C  
+ANISOU 3724  C   SER A 510    20455  19266  15554   5204  -1182  -2426       C  
+ATOM   3725  O   SER A 510      73.001  83.552   2.811  1.00140.49           O  
+ANISOU 3725  O   SER A 510    20177  18606  14598   5539  -1145  -2415       O  
+ATOM   3726  CB  SER A 510      70.807  85.999   2.911  1.00149.05           C  
+ANISOU 3726  CB  SER A 510    21111  19824  15699   5832   -930  -2348       C  
+ATOM   3727  OG  SER A 510      70.346  84.882   3.643  1.00147.27           O  
+ANISOU 3727  OG  SER A 510    21097  19617  15240   6154   -337  -1962       O  
+ATOM   3728  N   SER A 511      71.946  83.946   0.858  1.00139.39           N  
+ANISOU 3728  N   SER A 511    19184  18508  15269   4583  -1004  -2249       N  
+ATOM   3729  CA  SER A 511      72.011  82.573   0.365  1.00129.68           C  
+ANISOU 3729  CA  SER A 511    17763  17254  14255   4236   -745  -2013       C  
+ATOM   3730  C   SER A 511      73.437  82.171   0.006  1.00129.30           C  
+ANISOU 3730  C   SER A 511    17762  17135  14232   4035  -1175  -2258       C  
+ATOM   3731  O   SER A 511      73.792  80.991   0.047  1.00109.17           O  
+ANISOU 3731  O   SER A 511    15254  14565  11659   3957  -1019  -2119       O  
+ATOM   3732  CB  SER A 511      71.108  82.416  -0.862  1.00125.40           C  
+ANISOU 3732  CB  SER A 511    16701  16703  14243   3684   -564  -1828       C  
+ATOM   3733  OG  SER A 511      71.167  81.106  -1.394  1.00137.08           O  
+ANISOU 3733  OG  SER A 511    17990  18125  15969   3359   -392  -1635       O  
+ATOM   3734  N   GLN A 512      74.247  83.164  -0.347  1.00131.12           N  
+ANISOU 3734  N   GLN A 512    17958  17304  14560   3957  -1699  -2603       N  
+ATOM   3735  CA  GLN A 512      75.621  82.941  -0.774  1.00120.52           C  
+ANISOU 3735  CA  GLN A 512    16587  15845  13361   3755  -2110  -2821       C  
+ATOM   3736  C   GLN A 512      76.508  82.796   0.431  1.00123.24           C  
+ANISOU 3736  C   GLN A 512    17385  16120  13322   4264  -2359  -3023       C  
+ATOM   3737  O   GLN A 512      77.569  82.174   0.385  1.00128.94           O  
+ANISOU 3737  O   GLN A 512    18162  16749  14081   4188  -2573  -3124       O  
+ATOM   3738  CB  GLN A 512      76.096  84.150  -1.546  1.00118.44           C  
+ANISOU 3738  CB  GLN A 512    16077  15483  13440   3537  -2531  -3073       C  
+ATOM   3739  CG  GLN A 512      76.798  83.822  -2.807  1.00125.91           C  
+ANISOU 3739  CG  GLN A 512    16711  16343  14787   3048  -2644  -3057       C  
+ATOM   3740  CD  GLN A 512      76.915  85.020  -3.690  1.00137.22           C  
+ANISOU 3740  CD  GLN A 512    17859  17690  16589   2843  -2877  -3186       C  
+ATOM   3741  OE1 GLN A 512      77.456  86.052  -3.281  1.00153.03           O  
+ANISOU 3741  OE1 GLN A 512    19904  19568  18672   3053  -3245  -3442       O  
+ATOM   3742  NE2 GLN A 512      76.353  84.922  -4.897  1.00128.62           N  
+ANISOU 3742  NE2 GLN A 512    16487  16643  15739   2470  -2678  -3017       N  
+ATOM   3743  N   GLY A 513      76.073  83.422   1.510  1.00128.93           N  
+ANISOU 3743  N   GLY A 513    18453  16869  13665   4826  -2362  -3100       N  
+ATOM   3744  CA  GLY A 513      76.767  83.309   2.761  1.00135.31           C  
+ANISOU 3744  CA  GLY A 513    19790  17602  14021   5449  -2610  -3308       C  
+ATOM   3745  C   GLY A 513      76.597  81.908   3.295  1.00133.10           C  
+ANISOU 3745  C   GLY A 513    19748  17398  13425   5620  -2132  -3010       C  
+ATOM   3746  O   GLY A 513      77.464  81.407   3.988  1.00135.48           O  
+ANISOU 3746  O   GLY A 513    20407  17622  13448   5952  -2344  -3163       O  
+ATOM   3747  N   THR A 514      75.478  81.270   2.971  1.00130.00           N  
+ANISOU 3747  N   THR A 514    19139  17128  13128   5402  -1499  -2584       N  
+ATOM   3748  CA  THR A 514      75.252  79.899   3.409  1.00136.05           C  
+ANISOU 3748  CA  THR A 514    20053  17932  13707   5525   -990  -2248       C  
+ATOM   3749  C   THR A 514      76.125  78.980   2.571  1.00136.91           C  
+ANISOU 3749  C   THR A 514    19914  17993  14111   4991  -1151  -2279       C  
+ATOM   3750  O   THR A 514      76.451  77.859   2.971  1.00136.85           O  
+ANISOU 3750  O   THR A 514    20093  17981  13923   5102   -944  -2139       O  
+ATOM   3751  CB  THR A 514      73.784  79.475   3.234  1.00141.83           C  
+ANISOU 3751  CB  THR A 514    20522  18734  14631   5408   -287  -1768       C  
+ATOM   3752  OG1 THR A 514      73.591  78.921   1.927  1.00142.93           O  
+ANISOU 3752  OG1 THR A 514    20113  18858  15336   4676   -233  -1640       O  
+ATOM   3753  CG2 THR A 514      72.861  80.659   3.413  1.00145.09           C  
+ANISOU 3753  CG2 THR A 514    20916  19192  15018   5620   -214  -1761       C  
+ATOM   3754  N   ILE A 515      76.491  79.473   1.394  1.00129.08           N  
+ANISOU 3754  N   ILE A 515    18518  16960  13565   4442  -1494  -2442       N  
+ATOM   3755  CA  ILE A 515      77.327  78.735   0.468  1.00119.39           C  
+ANISOU 3755  CA  ILE A 515    17053  15677  12633   3951  -1657  -2465       C  
+ATOM   3756  C   ILE A 515      78.787  78.796   0.895  1.00127.05           C  
+ANISOU 3756  C   ILE A 515    18275  16524  13475   4143  -2161  -2798       C  
+ATOM   3757  O   ILE A 515      79.482  77.778   0.906  1.00128.44           O  
+ANISOU 3757  O   ILE A 515    18530  16671  13600   4065  -2153  -2760       O  
+ATOM   3758  CB  ILE A 515      77.220  79.308  -0.945  1.00110.42           C  
+ANISOU 3758  CB  ILE A 515    15452  14516  11987   3401  -1815  -2500       C  
+ATOM   3759  CG1 ILE A 515      75.801  79.150  -1.481  1.00109.39           C  
+ANISOU 3759  CG1 ILE A 515    15038  14466  12060   3177  -1388  -2203       C  
+ATOM   3760  CG2 ILE A 515      78.168  78.587  -1.861  1.00112.80           C  
+ANISOU 3760  CG2 ILE A 515    15581  14743  12533   2997  -1979  -2516       C  
+ATOM   3761  CD1 ILE A 515      75.570  79.879  -2.780  1.00110.01           C  
+ANISOU 3761  CD1 ILE A 515    14740  14519  12538   2759  -1561  -2268       C  
+ATOM   3762  N   GLU A 516      79.240  79.996   1.247  1.00122.76           N  
+ANISOU 3762  N   GLU A 516    17837  15878  12927   4400  -2627  -3132       N  
+ATOM   3763  CA  GLU A 516      80.636  80.218   1.589  1.00124.18           C  
+ANISOU 3763  CA  GLU A 516    18172  15860  13149   4571  -3208  -3493       C  
+ATOM   3764  C   GLU A 516      81.099  79.274   2.681  1.00126.09           C  
+ANISOU 3764  C   GLU A 516    18894  16095  12918   5029  -3183  -3522       C  
+ATOM   3765  O   GLU A 516      82.117  78.595   2.539  1.00116.84           O  
+ANISOU 3765  O   GLU A 516    17721  14825  11848   4893  -3381  -3605       O  
+ATOM   3766  CB  GLU A 516      80.863  81.656   2.046  1.00135.21           C  
+ANISOU 3766  CB  GLU A 516    19658  17112  14603   4907  -3722  -3854       C  
+ATOM   3767  CG  GLU A 516      82.315  82.045   1.962  1.00146.41           C  
+ANISOU 3767  CG  GLU A 516    20992  18238  16400   4885  -4381  -4215       C  
+ATOM   3768  CD  GLU A 516      82.865  81.775   0.582  1.00151.28           C  
+ANISOU 3768  CD  GLU A 516    21100  18789  17590   4220  -4329  -4073       C  
+ATOM   3769  OE1 GLU A 516      82.373  82.413  -0.367  1.00146.52           O  
+ANISOU 3769  OE1 GLU A 516    20133  18221  17316   3867  -4198  -3957       O  
+ATOM   3770  OE2 GLU A 516      83.763  80.917   0.441  1.00154.24           O  
+ANISOU 3770  OE2 GLU A 516    21471  19078  18055   4089  -4397  -4065       O  
+END                                                                             
diff --git a/examples/testdata/4IM2_missing_noid.pdb b/examples/testdata/4IM2_missing_noid.pdb
new file mode 100644
index 0000000..5a5ef94
--- /dev/null
+++ b/examples/testdata/4IM2_missing_noid.pdb
@@ -0,0 +1,524 @@
+TITLE     STRUCTURE OF TANK-BINDING KINASE 1  (Truncated test file)
+ATOM   3510  N   LEU A 468      76.337  90.332  -7.628  1.00168.53           N  
+ANISOU 3510  N   LEU A 468    19760  15191  29082   5189   1248  -1702       N  
+ATOM   3511  CA  LEU A 468      75.576  90.788  -6.476  1.00181.60           C  
+ANISOU 3511  CA  LEU A 468    21073  16927  30998   5158   1421  -2051       C  
+ATOM   3512  C   LEU A 468      76.285  91.971  -5.836  1.00196.57           C  
+ANISOU 3512  C   LEU A 468    23029  18636  33021   5053   1667  -2229       C  
+ATOM   3513  O   LEU A 468      75.727  93.067  -5.733  1.00197.97           O  
+ANISOU 3513  O   LEU A 468    23115  18581  33523   5166   1662  -2304       O  
+ATOM   3514  CB  LEU A 468      75.409  89.671  -5.449  1.00173.72           C  
+ANISOU 3514  CB  LEU A 468    19829  16340  29836   4981   1593  -2304       C  
+ATOM   3515  CG  LEU A 468      74.099  88.882  -5.420  1.00170.58           C  
+ANISOU 3515  CG  LEU A 468    19142  16142  29529   5074   1449  -2345       C  
+ATOM   3516  CD1 LEU A 468      74.023  87.940  -6.581  1.00167.98           C  
+ANISOU 3516  CD1 LEU A 468    18951  15858  29015   5180   1156  -2025       C  
+ATOM   3517  CD2 LEU A 468      73.988  88.096  -4.145  1.00165.16           C  
+ANISOU 3517  CD2 LEU A 468    18217  15818  28720   4865   1706  -2656       C  
+ATOM   3518  N   ASP A 469      77.529  91.753  -5.429  1.00208.80           N  
+ANISOU 3518  N   ASP A 469    24731  20282  34322   4836   1875  -2296       N  
+ATOM   3519  CA  ASP A 469      78.267  92.785  -4.720  1.00223.11           C  
+ANISOU 3519  CA  ASP A 469    26577  21960  36233   4701   2123  -2500       C  
+ATOM   3520  C   ASP A 469      78.653  93.973  -5.599  1.00231.96           C  
+ANISOU 3520  C   ASP A 469    27954  22654  37525   4817   2037  -2283       C  
+ATOM   3521  O   ASP A 469      78.718  95.100  -5.118  1.00235.71           O  
+ANISOU 3521  O   ASP A 469    28377  22940  38242   4798   2175  -2449       O  
+ATOM   3522  CB  ASP A 469      79.506  92.197  -4.057  1.00224.50           C  
+ANISOU 3522  CB  ASP A 469    26841  22370  36089   4433   2350  -2633       C  
+ATOM   3523  CG  ASP A 469      79.748  92.767  -2.679  1.00229.51           C  
+ANISOU 3523  CG  ASP A 469    27303  23107  36794   4254   2637  -3018       C  
+ATOM   3524  OD1 ASP A 469      79.958  93.992  -2.564  1.00232.36           O  
+ANISOU 3524  OD1 ASP A 469    27695  23203  37387   4262   2718  -3093       O  
+ATOM   3525  OD2 ASP A 469      79.751  91.979  -1.709  1.00229.48           O  
+ANISOU 3525  OD2 ASP A 469    27145  23450  36598   4098   2779  -3242       O  
+ATOM   3526  N   PHE A 470      78.904  93.735  -6.882  1.00233.88           N  
+ANISOU 3526  N   PHE A 470    28481  22742  37641   4931   1813  -1912       N  
+ATOM   3527  CA  PHE A 470      79.292  94.831  -7.766  1.00237.73           C  
+ANISOU 3527  CA  PHE A 470    29252  22819  38256   5033   1733  -1677       C  
+ATOM   3528  C   PHE A 470      78.103  95.470  -8.467  1.00232.15           C  
+ANISOU 3528  C   PHE A 470    28512  21868  37828   5322   1470  -1512       C  
+ATOM   3529  O   PHE A 470      78.021  96.691  -8.532  1.00230.69           O  
+ANISOU 3529  O   PHE A 470    28371  21372  37909   5402   1493  -1517       O  
+ATOM   3530  CB  PHE A 470      80.344  94.379  -8.784  1.00242.99           C  
+ANISOU 3530  CB  PHE A 470    30297  23410  38616   4976   1661  -1357       C  
+ATOM   3531  CG  PHE A 470      80.663  95.388  -9.839  1.00251.53           C  
+ANISOU 3531  CG  PHE A 470    31709  24074  39788   5089   1550  -1064       C  
+ATOM   3532  CD1 PHE A 470      81.658  96.315  -9.620  1.00252.90           C  
+ANISOU 3532  CD1 PHE A 470    32021  24036  40032   4942   1771  -1133       C  
+ATOM   3533  CD2 PHE A 470      80.005  95.389 -11.059  1.00255.02           C  
+ANISOU 3533  CD2 PHE A 470    32335  24339  40221   5330   1225   -715       C  
+ATOM   3534  CE1 PHE A 470      81.981  97.242 -10.575  1.00254.75           C  
+ANISOU 3534  CE1 PHE A 470    32569  23879  40344   5028   1688   -862       C  
+ATOM   3535  CE2 PHE A 470      80.321  96.320 -12.027  1.00256.76           C  
+ANISOU 3535  CE2 PHE A 470    32894  24173  40491   5427   1126   -433       C  
+ATOM   3536  CZ  PHE A 470      81.313  97.248 -11.784  1.00256.57           C  
+ANISOU 3536  CZ  PHE A 470    33006  23929  40550   5272   1365   -504       C  
+ATOM   3537  N   CYS A 471      77.190  94.665  -8.997  1.00176.88           N  
+ANISOU 3537  N   CYS A 471    20955  21812  24441   2225  -3821  -3711       N  
+ATOM   3538  CA  CYS A 471      76.124  95.233  -9.815  1.00176.41           C  
+ANISOU 3538  CA  CYS A 471    20820  21906  24301   2124  -3576  -3614       C  
+ATOM   3539  C   CYS A 471      74.868  95.631  -9.050  1.00176.82           C  
+ANISOU 3539  C   CYS A 471    21026  22206  23952   2247  -3588  -3734       C  
+ATOM   3540  O   CYS A 471      74.632  96.811  -8.854  1.00178.66           O  
+ANISOU 3540  O   CYS A 471    21175  22393  24314   2353  -3749  -3873       O  
+ATOM   3541  CB  CYS A 471      75.805  94.346 -11.019  1.00173.95           C  
+ANISOU 3541  CB  CYS A 471    20521  21694  23877   1925  -3217  -3359       C  
+ATOM   3542  SG  CYS A 471      76.954  94.571 -12.398  1.00273.04           S  
+ANISOU 3542  SG  CYS A 471    32850  33934  36957   1863  -3075  -3146       S  
+ATOM   3543  N   ILE A 472      74.068  94.670  -8.603  1.00173.50           N  
+ANISOU 3543  N   ILE A 472    20813  22023  23085   2253  -3402  -3662       N  
+ATOM   3544  CA  ILE A 472      72.771  95.033  -8.022  1.00171.09           C  
+ANISOU 3544  CA  ILE A 472    20616  21936  22453   2374  -3307  -3694       C  
+ATOM   3545  C   ILE A 472      72.832  96.022  -6.874  1.00177.82           C  
+ANISOU 3545  C   ILE A 472    21591  22750  23222   2698  -3611  -3931       C  
+ATOM   3546  O   ILE A 472      71.992  96.914  -6.776  1.00182.92           O  
+ANISOU 3546  O   ILE A 472    22220  23491  23792   2778  -3598  -3985       O  
+ATOM   3547  CB  ILE A 472      71.979  93.843  -7.518  1.00159.41           C  
+ANISOU 3547  CB  ILE A 472    19318  20653  20599   2393  -3038  -3546       C  
+ATOM   3548  CG1 ILE A 472      70.708  93.667  -8.341  1.00147.27           C  
+ANISOU 3548  CG1 ILE A 472    17653  19253  19051   2196  -2745  -3384       C  
+ATOM   3549  CG2 ILE A 472      71.526  94.090  -6.105  1.00155.95           C  
+ANISOU 3549  CG2 ILE A 472    19129  20312  19812   2752  -3085  -3637       C  
+ATOM   3550  CD1 ILE A 472      70.927  92.915  -9.606  1.00135.92           C  
+ANISOU 3550  CD1 ILE A 472    16097  17752  17794   1929  -2643  -3254       C  
+ATOM   3551  N   ARG A 473      73.812  95.865  -5.996  1.00180.33           N  
+ANISOU 3551  N   ARG A 473    22055  22917  23544   2920  -3920  -4092       N  
+ATOM   3552  CA  ARG A 473      73.860  96.762  -4.877  1.00189.65           C  
+ANISOU 3552  CA  ARG A 473    23415  24034  24610   3307  -4283  -4357       C  
+ATOM   3553  C   ARG A 473      74.328  98.021  -5.558  1.00185.98           C  
+ANISOU 3553  C   ARG A 473    22628  23344  24692   3195  -4530  -4477       C  
+ATOM   3554  O   ARG A 473      73.519  98.885  -5.866  1.00181.76           O  
+ANISOU 3554  O   ARG A 473    22002  22904  24153   3165  -4446  -4474       O  
+ATOM   3555  CB  ARG A 473      74.803  96.287  -3.768  1.00205.24           C  
+ANISOU 3555  CB  ARG A 473    25661  25862  26460   3635  -4629  -4545       C  
+ATOM   3556  CG  ARG A 473      74.468  96.921  -2.433  1.00220.50           C  
+ANISOU 3556  CG  ARG A 473    27955  27814  28011   4171  -4923  -4787       C  
+ATOM   3557  CD  ARG A 473      75.337  96.433  -1.295  1.00232.58           C  
+ANISOU 3557  CD  ARG A 473    29837  29192  29341   4591  -5300  -5003       C  
+ATOM   3558  NE  ARG A 473      76.763  96.602  -1.549  1.00237.46           N  
+ANISOU 3558  NE  ARG A 473    30220  29440  30564   4489  -5773  -5205       N  
+ATOM   3559  CZ  ARG A 473      77.716  95.991  -0.861  1.00240.32           C  
+ANISOU 3559  CZ  ARG A 473    30786  29623  30903   4725  -6098  -5371       C  
+ATOM   3560  NH1 ARG A 473      77.388  95.172   0.115  1.00241.12           N  
+ANISOU 3560  NH1 ARG A 473    31370  29900  30344   5100  -5978  -5355       N  
+ATOM   3561  NH2 ARG A 473      78.988  96.195  -1.159  1.00241.54           N  
+ANISOU 3561  NH2 ARG A 473    30651  29398  31724   4605  -6518  -5533       N  
+ATOM   3562  N   ASN A 474      75.608  98.073  -5.901  1.00188.74           N  
+ANISOU 3562  N   ASN A 474    22768  23381  25563   3107  -4772  -4534       N  
+ATOM   3563  CA  ASN A 474      76.168  99.264  -6.526  1.00188.61           C  
+ANISOU 3563  CA  ASN A 474    22395  23075  26194   3026  -4977  -4605       C  
+ATOM   3564  C   ASN A 474      75.420  99.892  -7.729  1.00173.98           C  
+ANISOU 3564  C   ASN A 474    20312  21326  24467   2781  -4623  -4414       C  
+ATOM   3565  O   ASN A 474      75.482 101.107  -7.891  1.00176.08           O  
+ANISOU 3565  O   ASN A 474    20374  21426  25104   2827  -4803  -4518       O  
+ATOM   3566  CB  ASN A 474      77.650  99.066  -6.857  1.00199.45           C  
+ANISOU 3566  CB  ASN A 474    23514  24060  28207   2939  -5170  -4595       C  
+ATOM   3567  CG  ASN A 474      78.504  98.809  -5.625  1.00210.23           C  
+ANISOU 3567  CG  ASN A 474    25062  25219  29597   3243  -5689  -4883       C  
+ATOM   3568  OD1 ASN A 474      78.174  99.240  -4.527  1.00215.26           O  
+ANISOU 3568  OD1 ASN A 474    25969  25891  29928   3596  -6043  -5160       O  
+ATOM   3569  ND2 ASN A 474      79.613  98.103  -5.810  1.00212.07           N  
+ANISOU 3569  ND2 ASN A 474    25176  25222  30179   3148  -5748  -4822       N  
+ATOM   3570  N   ILE A 475      74.722  99.114  -8.562  1.00161.86           N  
+ANISOU 3570  N   ILE A 475    18813  20033  22652   2556  -4165  -4158       N  
+ATOM   3571  CA  ILE A 475      74.022  99.727  -9.709  1.00154.84           C  
+ANISOU 3571  CA  ILE A 475    17755  19216  21861   2390  -3885  -4015       C  
+ATOM   3572  C   ILE A 475      72.785 100.520  -9.312  1.00159.27           C  
+ANISOU 3572  C   ILE A 475    18401  19995  22121   2490  -3891  -4125       C  
+ATOM   3573  O   ILE A 475      72.662 101.687  -9.663  1.00162.60           O  
+ANISOU 3573  O   ILE A 475    18651  20327  22804   2505  -3962  -4186       O  
+ATOM   3574  CB  ILE A 475      73.600  98.727 -10.818  1.00214.93           C  
+ANISOU 3574  CB  ILE A 475    25397  26975  29293   2173  -3475  -3753       C  
+ATOM   3575  CG1 ILE A 475      74.808  98.227 -11.613  1.00218.74           C  
+ANISOU 3575  CG1 ILE A 475    25753  27211  30145   2083  -3390  -3585       C  
+ATOM   3576  CG2 ILE A 475      72.618  99.379 -11.789  1.00210.37           C  
+ANISOU 3576  CG2 ILE A 475    24743  26509  28681   2097  -3256  -3677       C  
+ATOM   3577  CD1 ILE A 475      74.446  97.201 -12.664  1.00218.15           C  
+ANISOU 3577  CD1 ILE A 475    25777  27260  29850   1946  -3056  -3359       C  
+ATOM   3578  N   GLU A 476      71.856  99.893  -8.600  1.00156.45           N  
+ANISOU 3578  N   GLU A 476    18293  19907  21245   2571  -3778  -4120       N  
+ATOM   3579  CA  GLU A 476      70.623 100.594  -8.252  1.00142.72           C  
+ANISOU 3579  CA  GLU A 476    16627  18370  19231   2677  -3720  -4176       C  
+ATOM   3580  C   GLU A 476      70.845 101.560  -7.094  1.00144.41           C  
+ANISOU 3580  C   GLU A 476    16959  18500  19412   3012  -4114  -4440       C  
+ATOM   3581  O   GLU A 476      70.012 102.417  -6.811  1.00142.58           O  
+ANISOU 3581  O   GLU A 476    16768  18380  19024   3141  -4136  -4517       O  
+ATOM   3582  CB  GLU A 476      69.486  99.616  -7.958  1.00128.68           C  
+ANISOU 3582  CB  GLU A 476    15020  16860  17012   2665  -3395  -4018       C  
+ATOM   3583  CG  GLU A 476      69.562  98.905  -6.628  1.00128.73           C  
+ANISOU 3583  CG  GLU A 476    15321  16930  16662   2941  -3433  -4041       C  
+ATOM   3584  CD  GLU A 476      68.465  97.866  -6.484  1.00133.35           C  
+ANISOU 3584  CD  GLU A 476    15992  17719  16955   2900  -3026  -3806       C  
+ATOM   3585  OE1 GLU A 476      68.285  97.061  -7.422  1.00132.30           O  
+ANISOU 3585  OE1 GLU A 476    15710  17598  16962   2603  -2816  -3643       O  
+ATOM   3586  OE2 GLU A 476      67.768  97.860  -5.448  1.00136.37           O  
+ANISOU 3586  OE2 GLU A 476    16588  18223  17003   3196  -2912  -3773       O  
+ATOM   3587  N   LYS A 477      71.990 101.424  -6.439  1.00148.46           N  
+ANISOU 3587  N   LYS A 477    17534  18788  20087   3179  -4467  -4596       N  
+ATOM   3588  CA  LYS A 477      72.399 102.365  -5.405  1.00154.25           C  
+ANISOU 3588  CA  LYS A 477    18378  19348  20882   3544  -4976  -4907       C  
+ATOM   3589  C   LYS A 477      72.634 103.732  -5.994  1.00159.76           C  
+ANISOU 3589  C   LYS A 477    18754  19833  22117   3467  -5183  -5014       C  
+ATOM   3590  O   LYS A 477      72.568 104.742  -5.292  1.00158.01           O  
+ANISOU 3590  O   LYS A 477    18598  19516  21921   3749  -5568  -5266       O  
+ATOM   3591  CB  LYS A 477      73.667 101.883  -4.706  1.00154.03           C  
+ANISOU 3591  CB  LYS A 477    18446  19057  21022   3730  -5372  -5076       C  
+ATOM   3592  CG  LYS A 477      73.367 100.787  -3.750  1.00149.76           C  
+ANISOU 3592  CG  LYS A 477    18324  18717  19861   3975  -5258  -5042       C  
+ATOM   3593  CD  LYS A 477      74.437 100.554  -2.740  1.00143.39           C  
+ANISOU 3593  CD  LYS A 477    17737  17664  19082   4327  -5762  -5306       C  
+ATOM   3594  CE  LYS A 477      73.739 100.087  -1.488  1.00145.72           C  
+ANISOU 3594  CE  LYS A 477    18569  18186  18613   4805  -5697  -5337       C  
+ATOM   3595  NZ  LYS A 477      74.661  99.556  -0.469  1.00149.42           N  
+ANISOU 3595  NZ  LYS A 477    19366  18470  18936   5206  -6108  -5561       N  
+ATOM   3596  N   THR A 478      72.908 103.757  -7.293  1.00166.45           N  
+ANISOU 3596  N   THR A 478    19271  20589  23384   3124  -4918  -4810       N  
+ATOM   3597  CA  THR A 478      73.186 105.012  -7.968  1.00170.99           C  
+ANISOU 3597  CA  THR A 478    19509  20929  24531   3052  -5023  -4844       C  
+ATOM   3598  C   THR A 478      71.905 105.733  -8.391  1.00172.33           C  
+ANISOU 3598  C   THR A 478    19686  21358  24435   2999  -4780  -4796       C  
+ATOM   3599  O   THR A 478      71.021 105.170  -9.046  1.00163.10           O  
+ANISOU 3599  O   THR A 478    18581  20461  22928   2823  -4356  -4594       O  
+ATOM   3600  CB  THR A 478      74.217 104.856  -9.128  1.00146.93           C  
+ANISOU 3600  CB  THR A 478    16115  17589  22125   2815  -4843  -4626       C  
+ATOM   3601  OG1 THR A 478      74.873 106.106  -9.369  1.00147.15           O  
+ANISOU 3601  OG1 THR A 478    15790  17239  22881   2857  -5085  -4705       O  
+ATOM   3602  CG2 THR A 478      73.562 104.391 -10.425  1.00144.32           C  
+ANISOU 3602  CG2 THR A 478    15764  17473  21597   2570  -4282  -4318       C  
+ATOM   3603  N   VAL A 479      71.809 106.979  -7.944  1.00177.73           N  
+ANISOU 3603  N   VAL A 479    20309  21929  25291   3181  -5110  -5014       N  
+ATOM   3604  CA  VAL A 479      70.674 107.838  -8.218  1.00175.65           C  
+ANISOU 3604  CA  VAL A 479    20044  21875  24819   3171  -4959  -5013       C  
+ATOM   3605  C   VAL A 479      71.176 109.077  -8.939  1.00177.67           C  
+ANISOU 3605  C   VAL A 479    19928  21830  25749   3101  -5069  -5035       C  
+ATOM   3606  O   VAL A 479      72.353 109.417  -8.840  1.00179.02           O  
+ANISOU 3606  O   VAL A 479    19865  21600  26555   3150  -5387  -5121       O  
+ATOM   3607  CB  VAL A 479      69.983 108.266  -6.909  1.00168.37           C  
+ANISOU 3607  CB  VAL A 479    19442  21113  23418   3524  -5243  -5249       C  
+ATOM   3608  CG1 VAL A 479      69.008 109.403  -7.169  1.00162.23           C  
+ANISOU 3608  CG1 VAL A 479    18603  20470  22565   3531  -5176  -5285       C  
+ATOM   3609  CG2 VAL A 479      69.288 107.080  -6.256  1.00163.89           C  
+ANISOU 3609  CG2 VAL A 479    19236  20856  22180   3624  -4991  -5142       C  
+ATOM   3610  N   MET A 486      57.931 103.433  -6.150  1.00 92.00           N  
+ANISOU 3610  N   MET A 486    10154  13425  11375   3371  -1523  -3283       N  
+ATOM   3611  CA  MET A 486      56.824 104.104  -5.482  1.00110.61           C  
+ANISOU 3611  CA  MET A 486    12558  15882  13585   3644  -1287  -3161       C  
+ATOM   3612  C   MET A 486      56.182 105.150  -6.389  1.00111.38           C  
+ANISOU 3612  C   MET A 486    12428  16016  13877   3424  -1416  -3308       C  
+ATOM   3613  O   MET A 486      56.000 106.305  -6.002  1.00120.35           O  
+ANISOU 3613  O   MET A 486    13691  17243  14794   3639  -1526  -3430       O  
+ATOM   3614  CB  MET A 486      57.288 104.743  -4.170  1.00120.60           C  
+ANISOU 3614  CB  MET A 486    14253  17221  14347   4174  -1395  -3243       C  
+ATOM   3615  CG  MET A 486      58.405 105.768  -4.316  1.00126.87           C  
+ANISOU 3615  CG  MET A 486    15171  17987  15047   4196  -1944  -3629       C  
+ATOM   3616  SD  MET A 486      58.150 107.169  -3.210  1.00146.78           S  
+ANISOU 3616  SD  MET A 486    18044  20597  17128   4757  -2124  -3782       S  
+ATOM   3617  CE  MET A 486      58.003 106.326  -1.640  1.00102.35           C  
+ANISOU 3617  CE  MET A 486    12883  15002  11003   5391  -1797  -3524       C  
+ATOM   3618  N   GLY A 496      57.154  99.412  -2.065  1.00157.62           N  
+ANISOU 3618  N   GLY A 496    19150  21656  19083   4616     82  -2024       N  
+ATOM   3619  CA  GLY A 496      57.031  99.217  -3.498  1.00158.07           C  
+ANISOU 3619  CA  GLY A 496    18749  21636  19677   3991   -116  -2141       C  
+ATOM   3620  C   GLY A 496      57.664  97.914  -3.942  1.00163.71           C  
+ANISOU 3620  C   GLY A 496    19349  22235  20619   3709   -140  -2093       C  
+ATOM   3621  O   GLY A 496      58.040  97.090  -3.111  1.00167.17           O  
+ANISOU 3621  O   GLY A 496    20009  22652  20858   3970     79  -1915       O  
+ATOM   3622  N   GLU A 497      57.778  97.722  -5.254  1.00166.67           N  
+ANISOU 3622  N   GLU A 497    19413  22530  21383   3222   -403  -2250       N  
+ATOM   3623  CA  GLU A 497      58.431  96.534  -5.792  1.00170.73           C  
+ANISOU 3623  CA  GLU A 497    19840  22933  22098   2955   -485  -2239       C  
+ATOM   3624  C   GLU A 497      59.931  96.621  -5.556  1.00172.64           C  
+ANISOU 3624  C   GLU A 497    20403  23228  21965   3043   -809  -2472       C  
+ATOM   3625  O   GLU A 497      60.589  95.609  -5.311  1.00173.01           O  
+ANISOU 3625  O   GLU A 497    20547  23223  21965   3047   -764  -2395       O  
+ATOM   3626  CB  GLU A 497      58.173  96.394  -7.290  1.00169.62           C  
+ANISOU 3626  CB  GLU A 497    19361  22681  22408   2505   -727  -2374       C  
+ATOM   3627  CG  GLU A 497      56.882  97.012  -7.777  1.00173.11           C  
+ANISOU 3627  CG  GLU A 497    19518  23086  23171   2413   -663  -2350       C  
+ATOM   3628  CD  GLU A 497      56.703  96.840  -9.270  1.00173.61           C  
+ANISOU 3628  CD  GLU A 497    19329  23013  23621   2054   -974  -2531       C  
+ATOM   3629  OE1 GLU A 497      57.597  96.241  -9.908  1.00170.78           O  
+ANISOU 3629  OE1 GLU A 497    19040  22600  23250   1901  -1202  -2647       O  
+ATOM   3630  OE2 GLU A 497      55.672  97.300  -9.805  1.00174.73           O  
+ANISOU 3630  OE2 GLU A 497    19233  23093  24064   1967   -999  -2559       O  
+ATOM   3631  N   ILE A 498      60.466  97.836  -5.652  1.00171.44           N  
+ANISOU 3631  N   ILE A 498    20381  23149  21608   3107  -1147  -2757       N  
+ATOM   3632  CA  ILE A 498      61.883  98.078  -5.403  1.00167.93           C  
+ANISOU 3632  CA  ILE A 498    20186  22695  20926   3210  -1503  -2995       C  
+ATOM   3633  C   ILE A 498      62.251  97.620  -4.004  1.00173.82           C  
+ANISOU 3633  C   ILE A 498    21298  23465  21280   3659  -1379  -2903       C  
+ATOM   3634  O   ILE A 498      63.315  97.034  -3.789  1.00168.12           O  
+ANISOU 3634  O   ILE A 498    20732  22684  20462   3692  -1544  -2980       O  
+ATOM   3635  CB  ILE A 498      62.227  99.564  -5.520  1.00165.53           C  
+ANISOU 3635  CB  ILE A 498    19934  22420  20540   3287  -1855  -3283       C  
+ATOM   3636  CG1 ILE A 498      61.848 100.100  -6.901  1.00171.37           C  
+ANISOU 3636  CG1 ILE A 498    20360  23137  21618   2911  -1947  -3365       C  
+ATOM   3637  CG2 ILE A 498      63.706  99.798  -5.239  1.00153.61           C  
+ANISOU 3637  CG2 ILE A 498    18613  20820  18931   3398  -2256  -3525       C  
+ATOM   3638  CD1 ILE A 498      61.891 101.605  -6.996  1.00174.73           C  
+ANISOU 3638  CD1 ILE A 498    20793  23594  22004   2996  -2195  -3587       C  
+ATOM   3639  N   SER A 499      61.362  97.890  -3.054  1.00187.32           N  
+ANISOU 3639  N   SER A 499    23169  25252  22753   4049  -1074  -2727       N  
+ATOM   3640  CA  SER A 499      61.558  97.444  -1.683  1.00198.47           C  
+ANISOU 3640  CA  SER A 499    24999  26682  23729   4594   -880  -2593       C  
+ATOM   3641  C   SER A 499      61.611  95.926  -1.651  1.00206.95           C  
+ANISOU 3641  C   SER A 499    26003  27687  24943   4481   -548  -2315       C  
+ATOM   3642  O   SER A 499      62.302  95.334  -0.823  1.00211.11           O  
+ANISOU 3642  O   SER A 499    26867  28195  25151   4806   -533  -2293       O  
+ATOM   3643  CB  SER A 499      60.435  97.952  -0.780  1.00200.16           C  
+ANISOU 3643  CB  SER A 499    25385  26976  23690   5064   -498  -2368       C  
+ATOM   3644  OG  SER A 499      60.635  97.541   0.556  1.00203.12           O  
+ANISOU 3644  OG  SER A 499    26244  27359  23574   5697   -286  -2224       O  
+ATOM   3645  N   ASP A 500      60.877  95.300  -2.564  1.00209.43           N  
+ANISOU 3645  N   ASP A 500    25883  27938  25751   4040   -320  -2123       N  
+ATOM   3646  CA  ASP A 500      60.862  93.851  -2.655  1.00212.36           C  
+ANISOU 3646  CA  ASP A 500    26120  28207  26361   3883    -39  -1865       C  
+ATOM   3647  C   ASP A 500      62.097  93.307  -3.366  1.00203.21           C  
+ANISOU 3647  C   ASP A 500    24946  26999  25265   3557   -426  -2093       C  
+ATOM   3648  O   ASP A 500      62.511  92.195  -3.092  1.00204.96           O  
+ANISOU 3648  O   ASP A 500    25238  27165  25472   3573   -286  -1954       O  
+ATOM   3649  CB  ASP A 500      59.580  93.355  -3.335  1.00221.23           C  
+ANISOU 3649  CB  ASP A 500    26765  29217  28075   3573    287  -1593       C  
+ATOM   3650  CG  ASP A 500      58.346  93.583  -2.486  1.00233.55           C  
+ANISOU 3650  CG  ASP A 500    28310  30773  29657   3938    816  -1243       C  
+ATOM   3651  OD1 ASP A 500      58.502  93.807  -1.272  1.00239.09           O  
+ANISOU 3651  OD1 ASP A 500    29432  31558  29852   4492   1029  -1137       O  
+ATOM   3652  OD2 ASP A 500      57.226  93.532  -3.034  1.00237.24           O  
+ANISOU 3652  OD2 ASP A 500    28355  31128  30656   3709   1011  -1072       O  
+ATOM   3653  N   ILE A 501      62.692  94.094  -4.258  1.00192.67           N  
+ANISOU 3653  N   ILE A 501    23525  25673  24008   3292   -875  -2413       N  
+ATOM   3654  CA  ILE A 501      63.864  93.633  -5.007  1.00181.71           C  
+ANISOU 3654  CA  ILE A 501    22108  24215  22719   3006  -1195  -2587       C  
+ATOM   3655  C   ILE A 501      65.165  93.699  -4.196  1.00170.68           C  
+ANISOU 3655  C   ILE A 501    21064  22814  20972   3287  -1450  -2764       C  
+ATOM   3656  O   ILE A 501      65.940  92.735  -4.173  1.00164.70           O  
+ANISOU 3656  O   ILE A 501    20376  21999  20202   3222  -1476  -2736       O  
+ATOM   3657  CB  ILE A 501      64.023  94.385  -6.353  1.00138.03           C  
+ANISOU 3657  CB  ILE A 501    16341  18649  17453   2657  -1507  -2802       C  
+ATOM   3658  CG1 ILE A 501      63.385  93.589  -7.491  1.00130.33           C  
+ANISOU 3658  CG1 ILE A 501    15061  17587  16872   2296  -1411  -2683       C  
+ATOM   3659  CG2 ILE A 501      65.491  94.642  -6.682  1.00137.98           C  
+ANISOU 3659  CG2 ILE A 501    16437  18581  17410   2596  -1883  -3037       C  
+ATOM   3660  CD1 ILE A 501      61.877  93.516  -7.426  1.00127.50           C  
+ANISOU 3660  CD1 ILE A 501    14480  17217  16748   2292  -1111  -2482       C  
+ATOM   3661  N   HIS A 502      65.396  94.829  -3.532  1.00164.00           N  
+ANISOU 3661  N   HIS A 502    20439  22007  19869   3613  -1676  -2964       N  
+ATOM   3662  CA  HIS A 502      66.603  95.022  -2.737  1.00157.69           C  
+ANISOU 3662  CA  HIS A 502    19968  21147  18800   3931  -2029  -3195       C  
+ATOM   3663  C   HIS A 502      66.627  94.018  -1.594  1.00162.64           C  
+ANISOU 3663  C   HIS A 502    20933  21795  19069   4322  -1761  -3012       C  
+ATOM   3664  O   HIS A 502      67.677  93.496  -1.229  1.00164.35           O  
+ANISOU 3664  O   HIS A 502    21348  21935  19163   4433  -1971  -3125       O  
+ATOM   3665  CB  HIS A 502      66.654  96.452  -2.195  1.00150.83           C  
+ANISOU 3665  CB  HIS A 502    19272  20282  17755   4264  -2351  -3452       C  
+ATOM   3666  CG  HIS A 502      67.989  97.117  -2.348  1.00143.78           C  
+ANISOU 3666  CG  HIS A 502    18387  19223  17019   4248  -2929  -3804       C  
+ATOM   3667  ND1 HIS A 502      68.672  97.155  -3.544  1.00137.00           N  
+ANISOU 3667  ND1 HIS A 502    17193  18253  16609   3785  -3096  -3872       N  
+ATOM   3668  CD2 HIS A 502      68.759  97.787  -1.457  1.00140.15           C  
+ANISOU 3668  CD2 HIS A 502    18217  18647  16387   4674  -3387  -4099       C  
+ATOM   3669  CE1 HIS A 502      69.807  97.814  -3.383  1.00131.33           C  
+ANISOU 3669  CE1 HIS A 502    16503  17343  16055   3893  -3583  -4155       C  
+ATOM   3670  NE2 HIS A 502      69.883  98.208  -2.125  1.00130.34           N  
+ANISOU 3670  NE2 HIS A 502    16741  17200  15583   4416  -3815  -4326       N  
+ATOM   3671  N   THR A 503      65.450  93.751  -1.039  1.00163.37           N  
+ANISOU 3671  N   THR A 503    21080  21971  19022   4552  -1268  -2705       N  
+ATOM   3672  CA  THR A 503      65.295  92.771   0.033  1.00163.31           C  
+ANISOU 3672  CA  THR A 503    21384  21972  18696   4974   -872  -2437       C  
+ATOM   3673  C   THR A 503      65.393  91.327  -0.475  1.00151.49           C  
+ANISOU 3673  C   THR A 503    19659  20415  17484   4610   -614  -2206       C  
+ATOM   3674  O   THR A 503      65.955  90.464   0.198  1.00146.11           O  
+ANISOU 3674  O   THR A 503    19247  19705  16563   4853   -520  -2130       O  
+ATOM   3675  CB  THR A 503      63.956  92.972   0.783  1.00170.09           C  
+ANISOU 3675  CB  THR A 503    22342  22899  19387   5379   -334  -2106       C  
+ATOM   3676  OG1 THR A 503      64.026  94.162   1.576  1.00176.61           O  
+ANISOU 3676  OG1 THR A 503    23551  23775  19778   5902   -585  -2325       O  
+ATOM   3677  CG2 THR A 503      63.645  91.790   1.693  1.00171.53           C  
+ANISOU 3677  CG2 THR A 503    22747  23054  19374   5760    235  -1707       C  
+ATOM   3678  N   LYS A 504      64.865  91.071  -1.669  1.00141.41           N  
+ANISOU 3678  N   LYS A 504    17911  19106  16711   4058   -541  -2117       N  
+ATOM   3679  CA  LYS A 504      64.918  89.730  -2.251  1.00138.96           C  
+ANISOU 3679  CA  LYS A 504    17368  18711  16719   3706   -369  -1930       C  
+ATOM   3680  C   LYS A 504      66.335  89.382  -2.646  1.00142.04           C  
+ANISOU 3680  C   LYS A 504    17848  19062  17058   3520   -779  -2178       C  
+ATOM   3681  O   LYS A 504      66.762  88.230  -2.559  1.00134.46           O  
+ANISOU 3681  O   LYS A 504    16927  18053  16108   3463   -666  -2057       O  
+ATOM   3682  CB  LYS A 504      64.010  89.614  -3.477  1.00129.82           C  
+ANISOU 3682  CB  LYS A 504    15721  17488  16116   3223   -303  -1839       C  
+ATOM   3683  CG  LYS A 504      62.585  89.222  -3.164  1.00130.75           C  
+ANISOU 3683  CG  LYS A 504    15616  17544  16518   3307    225  -1458       C  
+ATOM   3684  N   LEU A 505      67.053  90.395  -3.100  1.00138.41           N  
+ANISOU 3684  N   LEU A 505    17394  18602  16593   3427  -1237  -2505       N  
+ATOM   3685  CA  LEU A 505      68.435  90.224  -3.458  1.00120.29           C  
+ANISOU 3685  CA  LEU A 505    15154  16230  14322   3285  -1619  -2726       C  
+ATOM   3686  C   LEU A 505      69.260  89.889  -2.223  1.00124.70           C  
+ANISOU 3686  C   LEU A 505    16126  16770  14484   3724  -1710  -2800       C  
+ATOM   3687  O   LEU A 505      70.166  89.052  -2.259  1.00124.02           O  
+ANISOU 3687  O   LEU A 505    16106  16619  14396   3643  -1808  -2823       O  
+ATOM   3688  CB  LEU A 505      68.966  91.499  -4.066  1.00109.42           C  
+ANISOU 3688  CB  LEU A 505    13673  14807  13094   3171  -2036  -3016       C  
+ATOM   3689  CG  LEU A 505      70.386  91.097  -4.404  1.00128.61           C  
+ANISOU 3689  CG  LEU A 505    16120  17111  15635   3034  -2336  -3157       C  
+ATOM   3690  CD1 LEU A 505      70.509  91.048  -5.920  1.00141.22           C  
+ANISOU 3690  CD1 LEU A 505    17393  18648  17616   2580  -2370  -3131       C  
+ATOM   3691  CD2 LEU A 505      71.441  91.946  -3.655  1.00114.58           C  
+ANISOU 3691  CD2 LEU A 505    14554  15224  13758   3350  -2784  -3462       C  
+ATOM   3692  N   LEU A 506      68.951  90.579  -1.132  1.00130.40           N  
+ANISOU 3692  N   LEU A 506    17159  17539  14847   4233  -1705  -2854       N  
+ATOM   3693  CA  LEU A 506      69.612  90.336   0.139  1.00131.63           C  
+ANISOU 3693  CA  LEU A 506    17798  17665  14549   4786  -1814  -2947       C  
+ATOM   3694  C   LEU A 506      69.501  88.865   0.507  1.00144.65           C  
+ANISOU 3694  C   LEU A 506    19548  19330  16080   4841  -1380  -2638       C  
+ATOM   3695  O   LEU A 506      70.448  88.287   1.024  1.00156.36           O  
+ANISOU 3695  O   LEU A 506    21304  20754  17351   5038  -1550  -2741       O  
+ATOM   3696  CB  LEU A 506      69.008  91.206   1.240  1.00120.17           C  
+ANISOU 3696  CB  LEU A 506    16713  16270  12675   5409  -1772  -2980       C  
+ATOM   3697  N   ARG A 507      68.351  88.260   0.214  1.00146.01           N  
+ANISOU 3697  N   ARG A 507    19470  19552  16453   4658   -839  -2263       N  
+ATOM   3698  CA  ARG A 507      68.159  86.831   0.443  1.00152.26           C  
+ANISOU 3698  CA  ARG A 507    20261  20320  17271   4649   -394  -1930       C  
+ATOM   3699  C   ARG A 507      69.164  86.004  -0.360  1.00145.14           C  
+ANISOU 3699  C   ARG A 507    19199  19352  16597   4200   -653  -2042       C  
+ATOM   3700  O   ARG A 507      69.471  84.873   0.007  1.00142.95           O  
+ANISOU 3700  O   ARG A 507    19044  19045  16224   4273   -450  -1882       O  
+ATOM   3701  CB  ARG A 507      66.724  86.401   0.111  1.00161.16           C  
+ANISOU 3701  CB  ARG A 507    21023  21434  18777   4463    165  -1523       C  
+ATOM   3702  CG  ARG A 507      65.661  86.975   1.046  1.00177.63           C  
+ANISOU 3702  CG  ARG A 507    23283  23565  20645   4978    585  -1290       C  
+ATOM   3703  CD  ARG A 507      64.263  86.468   0.696  1.00187.68           C  
+ANISOU 3703  CD  ARG A 507    24111  24757  22442   4769   1148   -857       C  
+ATOM   3704  NE  ARG A 507      63.229  87.082   1.527  1.00198.88           N  
+ANISOU 3704  NE  ARG A 507    25661  26202  23704   5259   1588   -600       N  
+ATOM   3705  CZ  ARG A 507      61.923  86.883   1.368  1.00205.71           C  
+ANISOU 3705  CZ  ARG A 507    26137  26967  25058   5169   2095   -210       C  
+ATOM   3706  NH1 ARG A 507      61.484  86.084   0.406  1.00207.33           N  
+ANISOU 3706  NH1 ARG A 507    25797  27020  25959   4610   2159    -75       N  
+ATOM   3707  NH2 ARG A 507      61.055  87.485   2.171  1.00208.11           N  
+ANISOU 3707  NH2 ARG A 507    26596  27293  25185   5668   2517     41       N  
+ATOM   3708  N   LEU A 508      69.681  86.579  -1.445  1.00134.19           N  
+ANISOU 3708  N   LEU A 508    17555  17933  15496   3776  -1072  -2294       N  
+ATOM   3709  CA  LEU A 508      70.654  85.888  -2.287  1.00125.06           C  
+ANISOU 3709  CA  LEU A 508    16259  16704  14555   3385  -1304  -2382       C  
+ATOM   3710  C   LEU A 508      72.070  85.983  -1.730  1.00133.75           C  
+ANISOU 3710  C   LEU A 508    17660  17739  15419   3609  -1705  -2655       C  
+ATOM   3711  O   LEU A 508      72.775  84.975  -1.650  1.00132.42           O  
+ANISOU 3711  O   LEU A 508    17581  17530  15202   3562  -1700  -2615       O  
+ATOM   3712  CB  LEU A 508      70.606  86.404  -3.726  1.00112.64           C  
+ANISOU 3712  CB  LEU A 508    14312  15095  13392   2907  -1513  -2482       C  
+ATOM   3713  CG  LEU A 508      69.271  86.186  -4.436  1.00113.17           C  
+ANISOU 3713  CG  LEU A 508    14056  15174  13769   2653  -1215  -2260       C  
+ATOM   3714  CD1 LEU A 508      69.459  86.184  -5.945  1.00106.22           C  
+ANISOU 3714  CD1 LEU A 508    12898  14225  13237   2216  -1432  -2343       C  
+ATOM   3715  CD2 LEU A 508      68.613  84.894  -3.968  1.00117.32           C  
+ANISOU 3715  CD2 LEU A 508    14560  15678  14341   2703   -779  -1932       C  
+ATOM   3716  N   SER A 509      72.491  87.188  -1.355  1.00130.72           N  
+ANISOU 3716  N   SER A 509    17414  17317  14936   3856  -2085  -2944       N  
+ATOM   3717  CA  SER A 509      73.767  87.347  -0.663  1.00136.66           C  
+ANISOU 3717  CA  SER A 509    18457  17948  15519   4156  -2531  -3236       C  
+ATOM   3718  C   SER A 509      73.698  86.583   0.646  1.00143.40           C  
+ANISOU 3718  C   SER A 509    19773  18845  15866   4687  -2319  -3138       C  
+ATOM   3719  O   SER A 509      74.680  85.977   1.082  1.00138.35           O  
+ANISOU 3719  O   SER A 509    19358  18121  15090   4839  -2521  -3256       O  
+ATOM   3720  CB  SER A 509      74.089  88.820  -0.410  1.00130.15           C  
+ANISOU 3720  CB  SER A 509    17685  17028  14738   4382  -3008  -3572       C  
+ATOM   3721  OG  SER A 509      74.991  89.319  -1.384  1.00125.27           O  
+ANISOU 3721  OG  SER A 509    16739  16248  14609   4003  -3376  -3749       O  
+ATOM   3722  N   SER A 510      72.520  86.615   1.263  1.00144.65           N  
+ANISOU 3722  N   SER A 510    20078  19123  15761   4999  -1878  -2899       N  
+ATOM   3723  CA  SER A 510      72.236  85.777   2.417  1.00148.97           C  
+ANISOU 3723  CA  SER A 510    21044  19713  15846   5526  -1487  -2677       C  
+ATOM   3724  C   SER A 510      72.424  84.315   2.046  1.00145.48           C  
+ANISOU 3724  C   SER A 510    20455  19266  15554   5204  -1182  -2426       C  
+ATOM   3725  O   SER A 510      73.001  83.552   2.811  1.00140.49           O  
+ANISOU 3725  O   SER A 510    20177  18606  14598   5539  -1145  -2415       O  
+ATOM   3726  CB  SER A 510      70.807  85.999   2.911  1.00149.05           C  
+ANISOU 3726  CB  SER A 510    21111  19824  15699   5832   -930  -2348       C  
+ATOM   3727  OG  SER A 510      70.346  84.882   3.643  1.00147.27           O  
+ANISOU 3727  OG  SER A 510    21097  19617  15240   6154   -337  -1962       O  
+ATOM   3728  N   SER A 511      71.946  83.946   0.858  1.00139.39           N  
+ANISOU 3728  N   SER A 511    19184  18508  15269   4583  -1004  -2249       N  
+ATOM   3729  CA  SER A 511      72.011  82.573   0.365  1.00129.68           C  
+ANISOU 3729  CA  SER A 511    17763  17254  14255   4236   -745  -2013       C  
+ATOM   3730  C   SER A 511      73.437  82.171   0.006  1.00129.30           C  
+ANISOU 3730  C   SER A 511    17762  17135  14232   4035  -1175  -2258       C  
+ATOM   3731  O   SER A 511      73.792  80.991   0.047  1.00109.17           O  
+ANISOU 3731  O   SER A 511    15254  14565  11659   3957  -1019  -2119       O  
+ATOM   3732  CB  SER A 511      71.108  82.416  -0.862  1.00125.40           C  
+ANISOU 3732  CB  SER A 511    16701  16703  14243   3684   -564  -1828       C  
+ATOM   3733  OG  SER A 511      71.167  81.106  -1.394  1.00137.08           O  
+ANISOU 3733  OG  SER A 511    17990  18125  15969   3359   -392  -1635       O  
+ATOM   3734  N   GLN A 512      74.247  83.164  -0.347  1.00131.12           N  
+ANISOU 3734  N   GLN A 512    17958  17304  14560   3957  -1699  -2603       N  
+ATOM   3735  CA  GLN A 512      75.621  82.941  -0.774  1.00120.52           C  
+ANISOU 3735  CA  GLN A 512    16587  15845  13361   3755  -2110  -2821       C  
+ATOM   3736  C   GLN A 512      76.508  82.796   0.431  1.00123.24           C  
+ANISOU 3736  C   GLN A 512    17385  16120  13322   4264  -2359  -3023       C  
+ATOM   3737  O   GLN A 512      77.569  82.174   0.385  1.00128.94           O  
+ANISOU 3737  O   GLN A 512    18162  16749  14081   4188  -2573  -3124       O  
+ATOM   3738  CB  GLN A 512      76.096  84.150  -1.546  1.00118.44           C  
+ANISOU 3738  CB  GLN A 512    16077  15483  13440   3537  -2531  -3073       C  
+ATOM   3739  CG  GLN A 512      76.798  83.822  -2.807  1.00125.91           C  
+ANISOU 3739  CG  GLN A 512    16711  16343  14787   3048  -2644  -3057       C  
+ATOM   3740  CD  GLN A 512      76.915  85.020  -3.690  1.00137.22           C  
+ANISOU 3740  CD  GLN A 512    17859  17690  16589   2843  -2877  -3186       C  
+ATOM   3741  OE1 GLN A 512      77.456  86.052  -3.281  1.00153.03           O  
+ANISOU 3741  OE1 GLN A 512    19904  19568  18672   3053  -3245  -3442       O  
+ATOM   3742  NE2 GLN A 512      76.353  84.922  -4.897  1.00128.62           N  
+ANISOU 3742  NE2 GLN A 512    16487  16643  15739   2470  -2678  -3017       N  
+ATOM   3743  N   GLY A 513      76.073  83.422   1.510  1.00128.93           N  
+ANISOU 3743  N   GLY A 513    18453  16869  13665   4826  -2362  -3100       N  
+ATOM   3744  CA  GLY A 513      76.767  83.309   2.761  1.00135.31           C  
+ANISOU 3744  CA  GLY A 513    19790  17602  14021   5449  -2610  -3308       C  
+ATOM   3745  C   GLY A 513      76.597  81.908   3.295  1.00133.10           C  
+ANISOU 3745  C   GLY A 513    19748  17398  13425   5620  -2132  -3010       C  
+ATOM   3746  O   GLY A 513      77.464  81.407   3.988  1.00135.48           O  
+ANISOU 3746  O   GLY A 513    20407  17622  13448   5952  -2344  -3163       O  
+ATOM   3747  N   THR A 514      75.478  81.270   2.971  1.00130.00           N  
+ANISOU 3747  N   THR A 514    19139  17128  13128   5402  -1499  -2584       N  
+ATOM   3748  CA  THR A 514      75.252  79.899   3.409  1.00136.05           C  
+ANISOU 3748  CA  THR A 514    20053  17932  13707   5525   -990  -2248       C  
+ATOM   3749  C   THR A 514      76.125  78.980   2.571  1.00136.91           C  
+ANISOU 3749  C   THR A 514    19914  17993  14111   4991  -1151  -2279       C  
+ATOM   3750  O   THR A 514      76.451  77.859   2.971  1.00136.85           O  
+ANISOU 3750  O   THR A 514    20093  17981  13923   5102   -944  -2139       O  
+ATOM   3751  CB  THR A 514      73.784  79.475   3.234  1.00141.83           C  
+ANISOU 3751  CB  THR A 514    20522  18734  14631   5408   -287  -1768       C  
+ATOM   3752  OG1 THR A 514      73.591  78.921   1.927  1.00142.93           O  
+ANISOU 3752  OG1 THR A 514    20113  18858  15336   4676   -233  -1640       O  
+ATOM   3753  CG2 THR A 514      72.861  80.659   3.413  1.00145.09           C  
+ANISOU 3753  CG2 THR A 514    20916  19192  15018   5620   -214  -1761       C  
+ATOM   3754  N   ILE A 515      76.491  79.473   1.394  1.00129.08           N  
+ANISOU 3754  N   ILE A 515    18518  16960  13565   4442  -1494  -2442       N  
+ATOM   3755  CA  ILE A 515      77.327  78.735   0.468  1.00119.39           C  
+ANISOU 3755  CA  ILE A 515    17053  15677  12633   3951  -1657  -2465       C  
+ATOM   3756  C   ILE A 515      78.787  78.796   0.895  1.00127.05           C  
+ANISOU 3756  C   ILE A 515    18275  16524  13475   4143  -2161  -2798       C  
+ATOM   3757  O   ILE A 515      79.482  77.778   0.906  1.00128.44           O  
+ANISOU 3757  O   ILE A 515    18530  16671  13600   4065  -2153  -2760       O  
+ATOM   3758  CB  ILE A 515      77.220  79.308  -0.945  1.00110.42           C  
+ANISOU 3758  CB  ILE A 515    15452  14516  11987   3401  -1815  -2500       C  
+ATOM   3759  CG1 ILE A 515      75.801  79.150  -1.481  1.00109.39           C  
+ANISOU 3759  CG1 ILE A 515    15038  14466  12060   3177  -1388  -2203       C  
+ATOM   3760  CG2 ILE A 515      78.168  78.587  -1.861  1.00112.80           C  
+ANISOU 3760  CG2 ILE A 515    15581  14743  12533   2997  -1979  -2516       C  
+ATOM   3761  CD1 ILE A 515      75.570  79.879  -2.780  1.00110.01           C  
+ANISOU 3761  CD1 ILE A 515    14740  14519  12538   2759  -1561  -2268       C  
+ATOM   3762  N   GLU A 516      79.240  79.996   1.247  1.00122.76           N  
+ANISOU 3762  N   GLU A 516    17837  15878  12927   4400  -2627  -3132       N  
+ATOM   3763  CA  GLU A 516      80.636  80.218   1.589  1.00124.18           C  
+ANISOU 3763  CA  GLU A 516    18172  15860  13149   4571  -3208  -3493       C  
+ATOM   3764  C   GLU A 516      81.099  79.274   2.681  1.00126.09           C  
+ANISOU 3764  C   GLU A 516    18894  16095  12918   5029  -3183  -3522       C  
+ATOM   3765  O   GLU A 516      82.117  78.595   2.539  1.00116.84           O  
+ANISOU 3765  O   GLU A 516    17721  14825  11848   4893  -3381  -3605       O  
+ATOM   3766  CB  GLU A 516      80.863  81.656   2.046  1.00135.21           C  
+ANISOU 3766  CB  GLU A 516    19658  17112  14603   4907  -3722  -3854       C  
+ATOM   3767  CG  GLU A 516      82.315  82.045   1.962  1.00146.41           C  
+ANISOU 3767  CG  GLU A 516    20992  18238  16400   4885  -4381  -4215       C  
+ATOM   3768  CD  GLU A 516      82.865  81.775   0.582  1.00151.28           C  
+ANISOU 3768  CD  GLU A 516    21100  18789  17590   4220  -4329  -4073       C  
+ATOM   3769  OE1 GLU A 516      82.373  82.413  -0.367  1.00146.52           O  
+ANISOU 3769  OE1 GLU A 516    20133  18221  17316   3867  -4198  -3957       O  
+ATOM   3770  OE2 GLU A 516      83.763  80.917   0.441  1.00154.24           O  
+ANISOU 3770  OE2 GLU A 516    21471  19078  18055   4089  -4397  -4065       O  
+END                                                                             
diff --git a/examples/testdata/4IM2_nterm.pdb b/examples/testdata/4IM2_nterm.pdb
new file mode 100644
index 0000000..48f7803
--- /dev/null
+++ b/examples/testdata/4IM2_nterm.pdb
@@ -0,0 +1,139 @@
+HEADER    TRANSFERASE/TRANSFERASE INHIBITOR       01-JAN-13   4IM2              
+TITLE     STRUCTURE OF TANK-BINDING KINASE 1  (Truncated test file)
+DBREF  4IM2 A    1   657  UNP    Q9UHD2   TBK1_HUMAN       1    657             
+SEQADV 4IM2 GLY A   -5  UNP  Q9UHD2              EXPRESSION TAG                 
+SEQADV 4IM2 SER A   -4  UNP  Q9UHD2              EXPRESSION TAG                 
+SEQADV 4IM2 GLY A   -3  UNP  Q9UHD2              EXPRESSION TAG                 
+SEQADV 4IM2 SER A   -2  UNP  Q9UHD2              EXPRESSION TAG                 
+SEQADV 4IM2 GLY A   -1  UNP  Q9UHD2              EXPRESSION TAG                 
+SEQADV 4IM2 SER A    0  UNP  Q9UHD2              EXPRESSION TAG                 
+SEQRES   1 A  663  GLY SER GLY SER GLY SER MET GLN SER THR SER ASN HIS
+ATOM      1  N   GLY A  -1     126.784   4.226 -23.353  1.00158.13           N  
+ANISOU    1  N   GLY A  -1    19370  17517  23197   6628   1162   2075       N  
+ATOM      2  CA  GLY A  -1     125.521   4.306 -24.062  1.00150.94           C  
+ANISOU    2  CA  GLY A  -1    18746  16231  22374   6153   1277   1996       C  
+ATOM      3  C   GLY A  -1     125.742   4.361 -25.557  1.00146.29           C  
+ANISOU    3  C   GLY A  -1    18187  15453  21943   5900   1405   1498       C  
+ATOM      4  O   GLY A  -1     126.691   4.980 -26.029  1.00150.85           O  
+ANISOU    4  O   GLY A  -1    18536  16366  22413   5906   1385   1160       O  
+ATOM      5  N   SER A   0     124.869   3.710 -26.313  1.00137.36           N  
+ANISOU    5  N   SER A   0    17328  13796  21068   5675   1550   1432       N  
+ATOM      6  CA  SER A   0     125.052   3.672 -27.755  1.00139.44           C  
+ANISOU    6  CA  SER A   0    17634  13884  21461   5464   1674    953       C  
+ATOM      7  C   SER A   0     123.846   4.104 -28.574  1.00137.43           C  
+ANISOU    7  C   SER A   0    17591  13478  21149   4975   1714    755       C  
+ATOM      8  O   SER A   0     122.737   4.275 -28.071  1.00128.25           O  
+ANISOU    8  O   SER A   0    16566  12244  19921   4780   1667    988       O  
+ATOM      9  CB  SER A   0     125.578   2.312 -28.214  1.00155.09           C  
+ANISOU    9  CB  SER A   0    19671  15395  23862   5752   1827    887       C  
+ATOM     10  OG  SER A   0     126.993   2.281 -28.131  1.00164.59           O  
+ANISOU   10  OG  SER A   0    20608  16866  25062   6113   1802    781       O  
+ATOM     11  N   MET A   1     124.096   4.270 -29.861  1.00134.87           N  
+ANISOU   11  N   MET A   1    17283  13123  20839   4799   1805    311       N  
+ATOM     12  CA  MET A   1     123.214   5.039 -30.698  1.00125.22           C  
+ANISOU   12  CA  MET A   1    16193  11958  19428   4369   1804     70       C  
+ATOM     13  C   MET A   1     122.885   4.351 -32.006  1.00124.69           C  
+ANISOU   13  C   MET A   1    16293  11510  19572   4225   1942   -293       C  
+ATOM     14  O   MET A   1     123.723   3.686 -32.606  1.00129.61           O  
+ANISOU   14  O   MET A   1    16868  11984  20394   4414   2057   -519       O  
+ATOM     15  CB  MET A   1     123.867   6.392 -30.970  1.00122.51           C  
+ANISOU   15  CB  MET A   1    15675  12140  18732   4254   1762   -132       C  
+ATOM     16  CG  MET A   1     125.074   6.368 -31.866  1.00120.74           C  
+ANISOU   16  CG  MET A   1    15318  12013  18544   4369   1884   -495       C  
+ATOM     17  SD  MET A   1     125.834   7.982 -31.850  1.00196.33           S  
+ANISOU   17  SD  MET A   1    24655  22193  27747   4246   1861   -642       S  
+ATOM     18  CE  MET A   1     126.785   7.896 -30.345  1.00132.53           C  
+ANISOU   18  CE  MET A   1    16264  14397  19693   4639   1728   -355       C  
+ATOM     19  N   GLN A   2     121.643   4.496 -32.440  1.00123.78           N  
+ANISOU   19  N   GLN A   2    16363  11253  19416   3898   1925   -369       N  
+ATOM     20  CA  GLN A   2     121.313   4.161 -33.809  1.00128.51           C  
+ANISOU   20  CA  GLN A   2    17093  11643  20094   3714   2020   -799       C  
+ATOM     21  C   GLN A   2     121.639   5.396 -34.617  1.00121.06           C  
+ANISOU   21  C   GLN A   2    16105  11138  18752   3541   2004  -1065       C  
+ATOM     22  O   GLN A   2     121.959   6.442 -34.059  1.00107.32           O  
+ANISOU   22  O   GLN A   2    14247   9790  16739   3528   1928   -906       O  
+ATOM     23  CB  GLN A   2     119.832   3.845 -33.965  1.00136.11           C  
+ANISOU   23  CB  GLN A   2    18240  12314  21161   3439   1994   -809       C  
+ATOM     24  CG  GLN A   2     119.171   3.277 -32.740  1.00148.45           C  
+ANISOU   24  CG  GLN A   2    19841  13613  22949   3500   1973   -376       C  
+ATOM     25  CD  GLN A   2     117.773   2.799 -33.042  1.00158.28           C  
+ANISOU   25  CD  GLN A   2    21243  14511  24385   3221   1993   -473       C  
+ATOM     26  OE1 GLN A   2     116.827   3.097 -32.313  1.00163.28           O  
+ANISOU   26  OE1 GLN A   2    21915  15160  24966   3070   1921   -211       O  
+ATOM     27  NE2 GLN A   2     117.631   2.057 -34.134  1.00155.02           N  
+ANISOU   27  NE2 GLN A   2    20902  13797  24200   3144   2095   -885       N  
+ATOM     28  N   SER A   3     121.547   5.280 -35.931  1.00124.66           N  
+ANISOU   28  N   SER A   3    16661  11530  19175   3410   2090  -1474       N  
+ATOM     29  CA  SER A   3     121.742   6.432 -36.781  1.00120.35           C  
+ANISOU   29  CA  SER A   3    16121  11369  18236   3242   2107  -1703       C  
+ATOM     30  C   SER A   3     121.190   6.186 -38.161  1.00125.27           C  
+ANISOU   30  C   SER A   3    16914  11882  18801   3073   2165  -2108       C  
+ATOM     31  O   SER A   3     120.746   5.090 -38.489  1.00135.86           O  
+ANISOU   31  O   SER A   3    18337  12848  20436   3082   2197  -2268       O  
+ATOM     32  CB  SER A   3     123.217   6.751 -36.923  1.00116.70           C  
+ANISOU   32  CB  SER A   3    15475  11153  17711   3435   2220  -1807       C  
+ATOM     33  OG  SER A   3     123.770   5.974 -37.974  1.00112.78           O  
+ANISOU   33  OG  SER A   3    15005  10478  17367   3528   2375  -2175       O  
+ATOM     34  N   THR A   4     121.244   7.232 -38.972  1.00116.48           N  
+ANISOU   34  N   THR A   4    15849  11109  17301   2928   2191  -2281       N  
+ATOM     35  CA  THR A   4     120.978   7.130 -40.394  1.00113.12           C  
+ANISOU   35  CA  THR A   4    15568  10691  16723   2823   2262  -2692       C  
+ATOM     36  C   THR A   4     122.118   7.839 -41.119  1.00116.32           C  
+ANISOU   36  C   THR A   4    15918  11410  16867   2884   2432  -2867       C  
+ATOM     37  O   THR A   4     123.106   8.236 -40.495  1.00117.17           O  
+ANISOU   37  O   THR A   4    15851  11671  16998   3007   2493  -2706       O  
+ATOM     38  CB  THR A   4     119.615   7.756 -40.775  1.00106.20           C  
+ANISOU   38  CB  THR A   4    14854   9927  15568   2568   2121  -2713       C  
+ATOM     39  OG1 THR A   4     119.774   9.154 -41.043  1.00107.14           O  
+ANISOU   39  OG1 THR A   4    15001  10451  15258   2480   2138  -2644       O  
+ATOM     40  CG2 THR A   4     118.597   7.567 -39.657  1.00 99.42           C  
+ANISOU   40  CG2 THR A   4    13990   8889  14896   2483   1956  -2396       C  
+ATOM     41  N   SER A   5     121.981   7.982 -42.432  1.00116.70           N  
+ANISOU   41  N   SER A   5    16106  11564  16670   2803   2517  -3210       N  
+ATOM     42  CA  SER A   5     122.975   8.671 -43.247  1.00122.60           C  
+ANISOU   42  CA  SER A   5    16837  12604  17144   2839   2721  -3385       C  
+ATOM     43  C   SER A   5     123.317  10.064 -42.713  1.00128.43           C  
+ANISOU   43  C   SER A   5    17501  13666  17630   2768   2748  -3105       C  
+ATOM     44  O   SER A   5     124.481  10.467 -42.712  1.00133.01           O  
+ANISOU   44  O   SER A   5    17934  14410  18193   2852   2925  -3133       O  
+ATOM     45  CB  SER A   5     122.473   8.779 -44.687  1.00127.34           C  
+ANISOU   45  CB  SER A   5    17646  13318  17418   2741   2774  -3729       C  
+ATOM     46  OG  SER A   5     121.108   9.163 -44.712  1.00135.31           O  
+ANISOU   46  OG  SER A   5    18807  14370  18235   2568   2576  -3643       O  
+ATOM     47  N   ASN A   6     122.303  10.783 -42.240  1.00122.78           N  
+ANISOU   47  N   ASN A   6    16868  13033  16750   2608   2581  -2859       N  
+ATOM     48  CA  ASN A   6     122.460  12.194 -41.897  1.00114.44           C  
+ANISOU   48  CA  ASN A   6    15777  12275  15429   2507   2620  -2639       C  
+ATOM     49  C   ASN A   6     122.348  12.537 -40.412  1.00108.55           C  
+ANISOU   49  C   ASN A   6    14870  11544  14832   2498   2474  -2282       C  
+ATOM     50  O   ASN A   6     122.712  13.640 -40.004  1.00110.16           O  
+ANISOU   50  O   ASN A   6    14983  11984  14890   2435   2531  -2135       O  
+ATOM     51  CB  ASN A   6     121.461  13.034 -42.695  1.00113.00           C  
+ANISOU   51  CB  ASN A   6    15832  12254  14850   2339   2583  -2658       C  
+ATOM     52  CG  ASN A   6     121.646  12.886 -44.191  1.00118.14           C  
+ANISOU   52  CG  ASN A   6    16648  12982  15257   2366   2743  -2999       C  
+ATOM     53  OD1 ASN A   6     122.765  12.952 -44.698  1.00122.16           O  
+ANISOU   53  OD1 ASN A   6    17097  13580  15737   2449   2985  -3154       O  
+ATOM     54  ND2 ASN A   6     120.546  12.672 -44.905  1.00118.96           N  
+ANISOU   54  ND2 ASN A   6    16946  13074  15179   2302   2609  -3139       N  
+ATOM     55  N   HIS A   7     121.845  11.605 -39.608  1.00100.48           N  
+ANISOU   55  N   HIS A   7    13810  10269  14098   2560   2305  -2149       N  
+ATOM     56  CA  HIS A   7     121.657  11.871 -38.183  1.00 91.49           C  
+ANISOU   56  CA  HIS A   7    12535   9160  13066   2569   2162  -1799       C  
+ATOM     57  C   HIS A   7     122.134  10.725 -37.300  1.00 97.74           C  
+ANISOU   57  C   HIS A   7    13180   9725  14232   2793   2117  -1685       C  
+ATOM     58  O   HIS A   7     122.456   9.647 -37.791  1.00101.23           O  
+ANISOU   58  O   HIS A   7    13643   9923  14898   2924   2188  -1876       O  
+ATOM     59  CB  HIS A   7     120.189  12.175 -37.884  1.00 86.30           C  
+ANISOU   59  CB  HIS A   7    12021   8464  12306   2383   1977  -1628       C  
+ATOM     60  CG  HIS A   7     119.634  13.303 -38.694  1.00101.46           C  
+ANISOU   60  CG  HIS A   7    14094  10603  13853   2201   2000  -1699       C  
+ATOM     61  ND1 HIS A   7     119.265  13.157 -40.015  1.00 99.83           N  
+ANISOU   61  ND1 HIS A   7    14076  10384  13472   2153   2049  -1976       N  
+ATOM     62  CD2 HIS A   7     119.401  14.600 -38.379  1.00 89.60           C  
+ANISOU   62  CD2 HIS A   7    12588   9342  12114   2078   1988  -1527       C  
+ATOM     63  CE1 HIS A   7     118.823  14.314 -40.476  1.00 97.86           C  
+ANISOU   63  CE1 HIS A   7    13944  10363  12875   2029   2062  -1939       C  
+ATOM     64  NE2 HIS A   7     118.896  15.206 -39.503  1.00 93.14           N  
+ANISOU   64  NE2 HIS A   7    13235   9899  12253   1975   2035  -1667       N  
+END                                                                             
diff --git a/examples/uniref50.hmm b/examples/uniref50.hmm
new file mode 100644
index 0000000..b07ec14
--- /dev/null
+++ b/examples/uniref50.hmm
@@ -0,0 +1,466 @@
+HMMER3/f [3.1b2 | February 2015]
+NAME  uniref50
+LENG  148 
+ALPH  amino
+ RF    no
+MM    no
+CONS  yes
+CS    no
+MAP   yes
+DATE  Mon Jun 12 14:32:05 2017
+NSEQ  15
+EFFN  0.648193
+CKSUM 2563184735
+STATS LOCAL MSV      -10.0682  0.70956
+STATS LOCAL VITERBI  -10.7870  0.70956
+STATS LOCAL FORWARD   -4.6837  0.70956
+HMM          A        C        D        E        F        G        H        I        K        L        M        N        P        Q        R        S        T        V        W        Y   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   2.40816  3.71583  2.80837  2.63551  3.47092  2.77036  3.85028  2.88279  2.80267  2.53589  3.68425  3.22102  3.34428  3.14560  3.11474  2.53177  2.75990  2.58070  5.00144  3.51101
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.10433  3.97705  2.52157  0.61958  0.77255  0.00000        *
+      1   2.99317  4.53706  4.08224  3.67789  3.22093  3.85692  4.40592  2.39958  3.44433  1.81088  1.32037  3.95163  4.31759  3.82413  3.64608  3.34553  3.29902  2.40928  5.06591  3.83044      1 m - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03044  3.90315  4.62550  0.61958  0.77255  0.55549  0.85282
+      2   0.97044  4.20710  3.49350  3.28598  4.08269  3.03087  4.30444  3.21278  3.30302  3.09300  4.12129  3.42792  3.77296  3.64134  3.55157  2.55705  2.83652  2.86187  5.50678  4.31039      2 a - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.11955  3.90315  2.38048  0.61958  0.77255  0.55549  0.85282
+      3   1.74035  4.09199  3.34495  3.00819  4.05288  2.91638  4.05509  3.33461  3.01251  3.11462  3.97728  3.20348  3.62940  3.32849  3.32799  1.99191  1.99086  2.89563  5.42641  4.20726      3 a - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03323  3.81683  4.53917  0.61958  0.77255  0.62561  0.76558
+      4   2.37663  4.18625  3.55838  3.17855  3.75132  3.18264  4.13666  2.64341  3.07328  2.62344  3.69712  3.39774  3.83139  3.44405  3.35689  2.61052  1.64486  2.15973  5.30034  4.05468      4 t - - -
+          2.68617  4.42230  2.77525  2.73129  3.46359  2.40511  3.72500  3.29359  2.67746  2.69350  4.24695  2.90352  2.73719  3.18152  2.89806  2.37885  2.77501  2.98524  4.58482  3.61508
+          0.33937  1.47682  2.82312  0.71438  0.67236  0.50642  0.92294
+      5   1.78828  4.31568  3.18846  2.75366  3.97645  3.11838  3.84000  3.34055  2.67250  3.02453  3.87541  3.10729  3.71676  3.06391  2.67828  2.15246  2.50645  2.96422  5.30410  4.05011      9 a - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03188  3.85742  4.57976  0.61958  0.77255  0.59400  0.80322
+      6   2.60146  4.34120  4.20318  3.64233  3.23200  4.03946  4.38229  1.91078  3.53317  1.46276  2.80385  3.95250  4.35454  3.78680  3.77614  3.34686  3.12310  1.90138  5.05979  3.90282     10 l - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03188  3.85742  4.57976  0.61958  0.77255  0.59400  0.80322
+      7   2.51618  4.38929  3.20785  2.68482  3.53842  3.39630  3.71025  2.97988  2.63127  2.66315  3.23915  3.11866  3.35060  2.98059  3.01133  2.11689  2.77574  2.72369  4.95633  3.10650     11 s - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03188  3.85742  4.57976  0.61958  0.77255  0.59400  0.80322
+      8   1.83112  4.12334  3.20156  2.95461  4.23963  1.79514  4.09699  3.64646  3.07597  3.33878  4.16582  3.16397  3.61350  3.35846  3.40724  1.96001  2.64648  3.10558  5.57497  4.34818     12 g - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.07518  3.85742  2.97012  0.61958  0.77255  0.59400  0.80322
+      9   2.02467  4.19921  3.47207  3.00878  3.03795  3.27081  3.95597  2.70270  2.96218  2.55248  3.54468  3.31239  3.83177  3.27950  3.28895  2.63385  2.09090  2.46488  5.06606  3.80489     13 a - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03327  3.81551  4.53786  0.61958  0.77255  0.56041  0.84624
+     10   2.25155  4.19461  3.85704  3.29295  2.92371  3.72128  4.04839  2.07964  3.20853  2.08962  2.71310  3.60847  4.09120  3.47607  3.47945  3.00735  2.74040  2.14097  4.86082  3.65928     14 i - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03170  3.86316  4.58551  0.61958  0.77255  0.53107  0.88667
+     11   2.97746  4.34766  4.53309  3.96552  2.78843  4.21079  4.53997  1.80103  3.85948  1.59494  2.57669  4.20401  4.48099  4.02954  4.02513  3.53069  3.20806  1.63119  5.03312  3.89134     15 l - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03044  3.90315  4.62550  0.61958  0.77255  0.55549  0.85282
+     12   2.01604  4.15364  3.23013  2.99255  4.26101  2.66741  4.12859  3.66796  3.09383  3.37186  4.20680  3.19709  3.64453  3.39377  3.41395  1.27425  2.68165  3.13093  5.59931  4.36607     16 s - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03044  3.90315  4.62550  0.61958  0.77255  0.55549  0.85282
+     13   2.41396  4.26265  3.40226  2.93569  3.72492  3.24366  3.92462  2.93397  2.83929  2.73560  3.16052  3.25846  3.81309  3.20648  3.16819  2.37913  1.73294  2.65776  5.16309  3.91530     17 t - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03044  3.90315  4.62550  0.61958  0.77255  0.55549  0.85282
+     14   2.06589  4.14828  3.30608  3.02868  4.20053  2.92394  4.12227  3.52677  3.06750  3.27902  4.13704  3.22373  3.65849  3.38850  3.37961  1.31011  2.40891  3.04032  5.55736  4.32788     18 s - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03044  3.90315  4.62550  0.61958  0.77255  0.55549  0.85282
+     15   2.74009  4.29274  3.92243  3.42912  1.74599  3.72053  3.90473  2.32427  3.32349  2.18956  3.31553  3.65797  4.14118  3.57919  3.55745  2.71376  3.01017  2.38146  4.46330  2.97696     19 f - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03044  3.90315  4.62550  0.61958  0.77255  0.55549  0.85282
+     16   2.76094  4.39380  4.31945  3.75589  3.18422  4.12530  4.45889  2.01307  3.63847  1.30728  2.59228  4.05575  4.41925  3.86957  3.85970  3.43754  3.19324  1.94550  5.06650  3.93230     20 l - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03044  3.90315  4.62550  0.61958  0.77255  0.55549  0.85282
+     17   2.70295  4.73637  3.16526  2.68917  4.18427  3.37581  3.71759  3.61851  2.27125  3.18722  4.06871  3.11427  2.39752  2.89725  1.66361  2.77186  2.98335  3.28411  5.34221  4.10051     21 r - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.07762  3.90315  2.90945  0.61958  0.77255  0.55549  0.85282
+     18   2.49055  4.81399  3.14505  2.59164  4.19520  3.44406  3.60132  3.55142  1.92611  3.12799  3.98038  3.04037  3.86298  2.75679  1.83484  2.76119  2.76042  3.23493  5.31169  4.06564     22 r - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.06501  3.85742  3.17445  0.61958  0.77255  0.59400  0.80322
+     19   2.43450  4.81939  2.81703  2.39298  4.15804  3.33308  3.59871  3.56807  2.06609  3.14527  3.97247  2.89702  3.36070  2.29211  2.66793  2.54254  2.87166  3.22778  5.35034  4.03520     23 k - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03294  3.82535  4.54770  0.61958  0.77255  0.61916  0.77305
+     20   2.61608  4.67386  2.79167  2.51004  4.07010  3.23635  3.73836  3.55025  2.48903  3.13320  4.04098  2.97430  2.02723  2.34075  2.83811  2.68076  2.93097  3.21608  5.34739  4.03735     24 p - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03294  3.82535  4.54770  0.61958  0.77255  0.51069  0.91649
+     21   1.83080  4.22890  3.60014  3.08598  3.61014  3.38577  4.01761  2.55536  3.00939  2.52819  3.20189  3.39791  3.91288  3.33215  3.33591  2.72706  2.41446  2.12040  5.12303  3.89826     25 a - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03044  3.90315  4.62550  0.61958  0.77255  0.55549  0.85282
+     22   2.43845  4.29437  3.39983  3.04145  3.80350  3.19872  4.06195  2.96220  2.98493  2.76612  3.80233  3.32666  1.71751  3.35496  3.29387  2.63325  2.83846  2.21304  5.28839  4.02321     26 p - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03044  3.90315  4.62550  0.61958  0.77255  0.55549  0.85282
+     23   2.55648  4.28453  3.47615  2.92649  3.45346  3.51308  3.86072  2.37030  2.85167  2.40896  2.93550  3.31525  2.97437  3.17776  3.19434  2.79032  2.33896  2.42929  4.94762  3.71651     27 t - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03044  3.90315  4.62550  0.61958  0.77255  0.55549  0.85282
+     24   2.23005  4.31546  3.25841  2.77512  3.78441  3.22479  3.82985  3.12652  2.73582  2.83244  3.03171  3.14960  3.26067  3.07830  3.10838  1.85715  2.73859  2.81468  5.16957  3.91289     28 s - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03044  3.90315  4.62550  0.61958  0.77255  0.55549  0.85282
+     25   2.72216  3.51794  4.14734  3.58168  3.26953  3.85722  4.23682  2.10046  3.47012  1.71220  2.91412  3.83361  4.22096  3.71804  3.68973  3.16541  2.79579  1.71693  4.93656  3.75086     29 l - - -
+          2.68606  4.42227  2.77522  2.73126  3.46337  2.40515  3.72497  3.29356  2.67743  2.69357  4.24692  2.90349  2.73742  3.18149  2.89784  2.37889  2.77522  2.98521  4.58479  3.61506
+          0.31572  1.55442  2.82310  0.27619  1.42159  0.55549  0.85282
+     26   2.06718  4.47388  3.00085  2.59301  4.03403  3.18938  3.75234  3.40130  2.21691  3.06406  3.90876  3.01767  3.74194  2.94856  2.91976  2.09488  2.60568  3.04014  5.32541  4.04568     31 a - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03205  3.85226  4.57460  0.61958  0.77255  0.52495  0.89548
+     27   2.09937  4.25808  3.35967  2.86682  3.65405  3.28224  3.85971  2.93650  2.81278  2.15397  3.59474  3.22143  3.43624  3.14697  3.16235  2.43009  2.43628  2.66078  5.07593  3.83686     32 a - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03044  3.90315  4.62550  0.61958  0.77255  0.55549  0.85282
+     28   2.56380  4.32380  3.45039  2.92280  3.52453  3.48960  3.88793  2.33272  2.83649  2.29194  3.45598  3.31192  2.56007  3.18425  3.18050  2.78603  2.52825  2.43071  5.02605  3.78340     33 l - - -
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+          0.03044  3.90315  4.62550  0.61958  0.77255  0.55549  0.85282
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+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.02889  3.95434  4.67668  0.61958  0.77255  0.50828  0.92013
+    122   2.37074  5.20065  2.03752  1.62561  4.52764  2.94012  3.68254  3.99698  2.59389  3.53203  4.34713  2.73405  3.79399  2.83254  3.13133  2.70217  3.03318  3.59496  5.71621  4.27884    130 e - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.02889  3.95434  4.67668  0.61958  0.77255  0.50828  0.92013
+    123   2.76891  4.53595  3.45942  3.36936  4.50963  0.61326  4.48439  4.12940  3.56175  3.77320  4.74981  3.62373  3.92970  3.87945  3.78857  2.94321  3.25651  3.64192  5.58291  4.61439    131 G - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.02889  3.95434  4.67668  0.61958  0.77255  0.50828  0.92013
+    124   3.45280  4.72560  4.55948  4.18538  1.45983  4.27876  3.45556  3.19175  4.01502  2.56322  3.77632  3.99268  4.58568  4.02082  4.06587  3.62371  3.67122  3.09770  1.76510  1.80304    132 f - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.02889  3.95434  4.67668  0.61958  0.77255  0.50828  0.92013
+    125   2.87283  4.39315  4.23821  3.90420  3.61058  3.80809  4.69198  2.04849  3.77322  2.28363  3.56364  4.08078  4.36427  4.12727  3.97777  3.31702  3.23254  0.92773  5.40873  4.14528    133 v - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.02889  3.95434  4.67668  0.61958  0.77255  0.50828  0.92013
+    126   3.24760  4.68579  4.32075  3.96132  3.16793  4.08580  4.59138  2.37683  3.72825  0.78064  3.16594  4.22883  4.50730  4.07699  3.89079  3.66669  3.53825  2.43535  5.07658  3.81868    134 l - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.02889  3.95434  4.67668  0.61958  0.77255  0.50828  0.92013
+    127   2.45786  4.30296  3.50186  3.25812  4.04222  3.13941  4.26905  3.17937  3.20271  3.03994  4.08552  3.45408  3.84975  3.59352  3.45722  2.66008  1.04037  2.86556  5.47283  4.25897    135 t - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.02889  3.95434  4.67668  0.61958  0.77255  0.50828  0.92013
+    128   2.68154  0.78852  4.21932  3.97783  3.95068  3.28696  4.60693  3.10838  3.80528  3.02007  4.14415  3.94300  4.00035  4.14805  3.91507  2.95331  3.15521  2.84739  5.34926  4.23772    136 c - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.02889  3.95434  4.67668  0.61958  0.77255  0.50828  0.92013
+    129   2.02617  4.29048  3.42265  2.94627  3.54036  3.40652  3.31257  2.77872  2.86355  2.59741  3.53948  3.30371  3.90044  3.21666  3.18816  2.73904  2.82169  1.86270  5.00831  3.74432    137 v - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.02889  3.95434  4.67668  0.61958  0.77255  0.50828  0.92013
+    130   0.90195  4.23400  3.54659  3.34205  4.13472  3.05626  4.35430  3.27256  3.36043  3.15035  4.17350  3.47069  3.80326  3.69417  3.60509  2.58374  2.86679  2.91280  5.55371  4.36315    138 a - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.02889  3.95434  4.67668  0.61958  0.77255  0.50828  0.92013
+    131   3.44381  4.80306  4.30117  3.95207  1.85364  4.19548  3.48537  3.22033  3.81418  2.60484  3.85318  3.90681  4.54641  3.92239  3.94488  3.57229  3.68268  3.12961  3.68006  0.97942    139 y - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.02889  3.95434  4.67668  0.61958  0.77255  0.50828  0.92013
+    132   2.86235  4.60578  3.47842  3.32948  4.31715  3.28867  4.39999  3.88386  3.39382  3.50174  4.55528  3.62780  0.68858  3.78012  3.62986  3.03247  3.31042  3.51987  5.48103  4.43903    140 P - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.02889  3.95434  4.67668  0.61958  0.77255  0.50828  0.92013
+    133   2.60256  4.60991  3.08123  2.59418  3.90705  3.39886  3.69738  3.25085  2.27951  2.91739  3.78849  3.05676  3.84470  2.63540  2.79735  2.69573  1.94572  2.76699  5.21418  3.93668    141 t - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.02889  3.95434  4.67668  0.61958  0.77255  0.50828  0.92013
+    134   2.16968  3.47307  3.59233  3.22260  4.15866  2.47411  4.19438  3.56363  3.18625  3.27458  4.10858  3.32406  3.66022  3.48496  3.48055  1.23700  2.65371  3.05043  5.52336  4.31592    142 s - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.02889  3.95434  4.67668  0.61958  0.77255  0.50828  0.92013
+    135   3.07859  5.21813  0.80740  2.38838  4.60638  3.27362  4.00471  4.21341  3.10456  3.80732  4.78755  2.94873  3.93224  3.24424  3.63163  3.03196  3.41903  3.84400  5.75900  4.46621    143 d - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.02889  3.95434  4.67668  0.61958  0.77255  0.50828  0.92013
+    136   2.87283  4.39315  4.23821  3.90420  3.61058  3.80809  4.69198  2.04849  3.77322  2.28363  3.56364  4.08078  4.36427  4.12727  3.97777  3.31702  3.23254  0.92773  5.40873  4.14528    144 v - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.02889  3.95434  4.67668  0.61958  0.77255  0.50828  0.92013
+    137   2.50102  4.23694  3.76525  3.33965  3.72246  3.37067  4.24809  2.46042  3.23911  2.55924  3.64161  3.56053  3.97799  3.58142  3.52035  2.77764  1.69802  1.75863  5.30971  4.08018    145 t - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.02889  3.95434  4.67668  0.61958  0.77255  0.50828  0.92013
+    138   3.09498  4.49149  4.45102  4.07022  3.43002  4.15408  4.78347  0.98199  3.89992  1.99977  3.35310  4.30411  4.57779  4.24002  4.08717  3.65761  3.39284  1.85079  5.33749  4.08258    146 i - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.02889  3.95434  4.67668  0.61958  0.77255  0.50828  0.92013
+    139   3.02382  5.15051  2.52384  0.91441  4.50717  3.32764  3.92196  3.97736  2.81286  3.58149  4.55225  2.98104  3.93620  3.13613  3.22992  2.99812  3.32879  3.65289  5.66334  4.38601    147 e - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.02889  3.95434  4.67668  0.61958  0.77255  0.50828  0.92013
+    140   2.45786  4.30296  3.50186  3.25812  4.04222  3.13941  4.26905  3.17937  3.20271  3.03994  4.08552  3.45408  3.84975  3.59352  3.45722  2.66008  1.04037  2.86556  5.47283  4.25897    148 t - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.02889  3.95434  4.67668  0.61958  0.77255  0.50828  0.92013
+    141   3.08695  4.88934  3.20791  2.97643  3.34377  3.51816  0.98092  3.80251  2.81733  3.28606  4.33566  3.38232  4.07539  3.34383  3.07797  3.15699  3.39324  3.53609  4.80769  3.29239    149 h - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.02889  3.95434  4.67668  0.61958  0.77255  0.50828  0.92013
+    142   2.99214  5.06805  3.26268  2.74531  4.47846  3.57206  3.65342  3.86981  1.12103  3.36156  4.25702  3.16311  3.99796  2.80635  2.11223  3.00404  3.19554  3.55761  5.42835  4.23089    150 k - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.02889  3.95434  4.67668  0.61958  0.77255  0.50828  0.92013
+    143   3.02382  5.15051  2.52384  0.91441  4.50717  3.32764  3.92196  3.97736  2.81286  3.58149  4.55225  2.98104  3.93620  3.13613  3.22992  2.99812  3.32879  3.65289  5.66334  4.38601    151 e - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.02889  3.95434  4.67668  0.61958  0.77255  0.50828  0.92013
+    144   2.49167  5.21869  2.13891  1.38935  4.54510  3.23855  3.71342  3.98470  2.64038  3.55288  4.39217  2.73628  3.81159  2.87379  3.17028  2.74234  3.08340  3.59770  5.74876  4.31122    152 e - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.02889  3.95434  4.67668  0.61958  0.77255  0.50828  0.92013
+    145   2.67924  5.36825  1.81597  1.42545  4.67130  3.22067  3.71949  4.14895  2.68617  3.67868  4.51726  2.69278  3.81366  2.87890  3.25116  2.76699  3.13943  3.73938  5.85528  4.37934    153 e - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.02889  3.95434  4.67668  0.61958  0.77255  0.50828  0.92013
+    146   3.24708  4.60677  4.69416  4.13988  3.08947  4.47063  4.76500  1.92492  3.96672  0.95356  2.71915  4.43331  4.67883  4.15873  4.13317  3.81764  3.47493  2.15974  5.15578  4.04247    154 l - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.02889  3.95434  4.67668  0.61958  0.77255  0.50828  0.92013
+    147   2.69781  4.29649  3.84369  3.29786  3.44437  3.73086  4.15124  2.24231  3.19336  2.10104  3.11890  3.63278  4.14347  3.51043  3.49251  3.03876  2.03846  1.78833  5.07714  3.86271    155 v - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.18495  3.95434  1.89921  0.61958  0.77255  0.50828  0.92013
+    148   1.44115  4.10304  3.22225  2.99375  4.15355  2.08176  4.10711  3.47540  3.09081  3.24183  4.11431  3.18864  3.61518  3.39097  3.39593  2.35434  2.65737  2.99565  5.50492  4.29375    156 a - - -
+          2.68608  4.42226  2.77520  2.73124  3.46354  2.40513  3.72495  3.29355  2.67741  2.69355  4.24690  2.90347  2.73740  3.18147  2.89801  2.37887  2.77520  2.98519  4.58477  3.61504
+          0.08120  2.55114        *  0.46726  0.98542  0.00000        *
+//
diff --git a/help/help.jhm b/help/help.jhm
index 732f01b..506b3f3 100755
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -22,7 +22,7 @@
    <mapID target="home" url="html/index.html" />
    
    <mapID target="new" url="html/whatsNew.html"/>
-   <mapID target="release" url="html/releases.html#Jalview.2.10.3b1"/>
+   <mapID target="release" url="html/releases.html#Jalview.2.10.4"/>
    <mapID target="alannotation" url="html/features/annotation.html"/>
    <mapID target="keys" url="html/keys.html"/>
    <mapID target="newkeys" url="html/features/newkeystrokes.html"/>
@@ -126,6 +126,7 @@
    <mapID target="alwCalc" url="html/menus/alwcalculate.html"/>
    
    <mapID target="wsMenu" url="html/menus/wsmenu.html"/>
+   <mapID target="alwHmmer" url="html/menus/alwhmmer.html"/>
    <mapID target="popMenu" url="html/menus/popupMenu.html"/>
    <mapID target="popMenuAddref" url="html/menus/popupMenu.html#addrefannot"/>
    <mapID target="annotPanelMenu" url="html/menus/alwannotationpanel.html"/>
diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 20dd8db..71b7ef9 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -152,6 +152,7 @@
 				<tocitem text="Colour Menu" target="alwColour" />
 				<tocitem text="Calculate Menu" target="alwCalc" />
 				<tocitem text="Web Service Menu" target="wsMenu" />
+				<tocitem text="HMMER Menu" target="alwHmmer" />
 				<tocitem text="Annotation Panel Menu" target="annotPanelMenu" />
 				<tocitem text="Popup Menu" target="popMenu" />
 			</tocitem>
diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html
index b29b66b..533af5c 100755
--- a/help/html/features/preferences.html
+++ b/help/html/features/preferences.html
@@ -62,8 +62,10 @@
       sequence alignments and EPS files.
     </li>
     <li>The <a href="#editing"><strong>&quot;Editing&quot;</strong>
-        Preferences</a> tab contains settings affecting the export of
-      sequence alignments and EPS files.
+        Preferences</a> tab contains settings affecting the behaviour of alignments as you edit them.
+    </li>
+    <li>The <a href="#hmmer"><strong>&quot;HMMER&quot;</strong>
+        Preferences</a> tab allows you to configure locally installed HMMER tools.
     </li>
     <li>The <a href="dassettings.html"><strong>&quot;DAS
           Settings&quot;</strong> Preferences</a> tab allows you to select which DAS
@@ -387,7 +389,13 @@
     <em>Sort with New Tree</em> - When selected, any trees calculated or
     loaded onto the alignment will automatically sort the alignment.
   </p>
-  <p>&nbsp;</p>
-  <p>&nbsp;</p>
+  <p>
+    <a name="hmmer"><strong>&quot;HMMER&quot; Preferences tab</strong></a>
+  </p>
+  <p>If you have installed HMMER tools (available from <a href="http://hmmerorg">hmmer.org</a>),
+  then you should specify on this screen the location of the installation (the path to the folder 
+  containing binary executable programs). Double-click in the input field to open a file browser.</p>
+  <p>When this path is configured, the <a href="../menus/alwhmmer.html">HMMER menu</a> will be
+  enabled in the Alignment window.</p>
 </body>
 </html>
diff --git a/help/html/features/splitView.html b/help/html/features/splitView.html
index be1bd66..e1c07c1 100644
--- a/help/html/features/splitView.html
+++ b/help/html/features/splitView.html
@@ -76,7 +76,7 @@
       or <strong>"View&#8594;Nucleotide"</strong> (in the protein panel)
       allows you to show or hide one or other of the linked alignment
       panels.</li>
-    <li>Panel heights are adjusted dragging the divider between
+    <li>Panel heights are adjusted by dragging the divider between
       them using the mouse</li>
     <li><a href="../menus/alwview.html"><strong>"View&#8594;New
           View / Expand Views / Gather Views"</strong></a> behave as for a normal
diff --git a/help/html/menus/alwhmmer.html b/help/html/menus/alwhmmer.html
new file mode 100644
index 0000000..ce23c4b
--- /dev/null
+++ b/help/html/menus/alwhmmer.html
@@ -0,0 +1,87 @@
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+</head>
+<body>
+<p>
+  <strong>HMMER Menu</strong>
+</p>
+<p>This menu is available if hmmbuild tools have been installed and configured in the 
+<a href="../features/preferences.html#hmmer">HMMER Preferences</a> panel.
+  <br><br>
+  
+  <strong>hmmbuild</strong>
+  <br><br>Run hmmbuild to create a Hidden Markov Model profile of your sequence alignment or sub-groups.
+  <br><br>The consensus sequence for the computed profile is inserted as the first sequence of
+  the alignment (or group) for which hmmbuild is run.
+  <br>Jalview also computes and displays an annotation below the alignment, showing
+  the information content of each column.
+  <br>This is calculated as the sum over residue symbols of
+  <pre>
+    match emission probability * log(match emission probability / background frequency) / log(2)
+  </pre>
+  where the background frequencies are taken from (tbc: where? not https://www.ebi.ac.uk/uniprot/TrEMBLstats)
+  <ul>
+  <li>Edit settings and run...
+  <br><br>Choose whether to run hmmbuild for the whole alignment, or all or selected groups, or both 
+  (default is the alignment).
+  <br>Optionally enter a name to give the HMM profile consensus sequence
+  (default is "Alignment" or group name, with "_HMM" appended).
+  <br>Use Reference Annotation: select this option if your alignment has an RF reference annotation,
+  and you wish to constrain the HMM profile to it (hmmbuild option '--hand').
+  <br><br></li>
+  <li>hmmbuild with default settings
+  <br><br>Runs hmmbuild for the whole alignment.</li>
+  </ul>
+  
+  <strong>hmmalign</strong> and <strong>hmmsearch</strong> require an HMM consensus sequence to be selected first.
+  <br><em>To do this, right-click on the name of an HMM sequence added by hmmbuild, and 'Select HMM'.
+  The alignment will be with respect to the HMM profile for the consensus sequence.</em>
+  <br><br>
+  <strong>hmmalign</strong>
+  <br><br>Run hmmalign to align selected sequences (or the whole alignment) to a selected HMM profile.
+  <ul>
+  <li>Edit settings and run...
+  <br><br>Choose whether to 'trim non-matching termini' - hmmalign option '--trim'.
+  <br><br></li>
+  <li>hmmalign with default settings</li>
+  </ul>
+  <strong>hmmsearch</strong>
+  <br><br>Run hmmsearch to use an HMM profile as input to search a sequence database.
+  <ul>
+  <li>Edit settings and run...
+  <ul>
+  <li>tbc: choose database</li>
+  <li>tbc: automatically align</li>
+  <li>tbc: return accessions</li>
+  <li>tbc: number of results</li>
+  <li>tbc: sequence eValue cutoff</li>
+  <li>tbc: domains eValue cutoff</li>
+  </ul>
+  </li>
+  <br><li>hmmsearch with default settings</li>
+  <br><li>Add database
+  <br>Browse to select a local sequence data file to be searched</li>
+  </ul>
+<br>
+</body>
+</html>
diff --git a/help/html/releases.html b/help/html/releases.html
index 83d2ce4..006ee5c 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -70,6 +70,44 @@ li:before {
     <tr>
       <td width="60" nowrap>
         <div align="center">
+          <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>27/02/2018</em></strong>
+        </div>
+      </td>
+      <td><div align="left">
+          <em></em>
+          <ul>
+            <li>
+              <!-- JAL-984 -->Mouse cursor changes to indicate Sequence ID and annotation area margins can be click-dragged to adjust them.</li> 
+            <li>
+            <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and Ensembl services 
+            </li>
+            <li>
+            <!-- JAL-2759 -->Improved performance for large alignments and lots of hidden columns
+            </li>
+          </ul>
+          </div>
+      </td>
+      <td><div align="left">
+          <ul>
+            <li>
+              <!-- JAL-2778 -->Slow redraw when Overview panel shown overlapping alignment panel
+            </li>
+            <li>
+              <!-- JAL-2666 -->Linked scrolling via protein horizontal scroll bar doesn't work for some CDS/Protein views 
+            </li>
+            <li><!-- JAL-2930 -->Trackpad scrolling is broken on OSX on Java 1.8u153 onwards and Java 1.9u4+.</li>
+            <li><!-- JAL-2924 -->Tooltip shouldn't be displayed for empty columns in annotation row</li>
+            <li><!-- JAL-2913 -->Preferences panel's ID Width control is honored in interactive and batch mode</li>
+            </ul><em>Applet</em><ul>
+            <li><!-- JAL-2926 -->Copy consensus sequence option in applet should copy the group consensus when popup is opened on it</li>
+             
+          </ul>
+      </div>
+      </td>
+    </tr>
+    <tr>
+      <td width="60" nowrap>
+        <div align="center">
           <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
         </div>
       </td>
diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index 6d75f0f..d3972f5 100755
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -24,25 +24,15 @@
 </head>
 <body>
   <p>
-    <strong>What's new in Jalview 2.10.3b1 ?</strong>
+    <strong>What's new in Jalview 2.10.4 ?</strong>
   </p>
   <p>
-    This is the January 2018 patch release, which addresses critical bugs including trackpad function in OSX, and display of multiple 3D structures. 
-    The full list bugs fixed in this release can be found in the <a href="releases.html#Jalview.2.10.3b1">2.10.3b1
-      Release Notes</a>. In addition, Jalview 2.10.3 provides:
+    This is the February 2018 release of Jalview, with several minor bug fixes and enhanvements. 
+    The full list bugs fixed in this release can be found in the <a href="releases.html#Jalview.2.10.4">2.10.4
+      Release Notes</a>. In addition, Jalview 2.10.4 provides:
   </p>
   <ul>
-    <li>Faster and more responsive UI when importing and working
-      with wide alignments and handling hundreds and thousands of
-      sequence features</li>
-    <li>Improved usability with <a
-      href="features/pdbsequencefetcher.html">PDB</a> and <a
-      href="features/uniprotsequencefetcher.html">UniProt</a> Free Text
-      Search dialog, and new tab for retrieval of sequences for lists of
-      IDs.
-    </li>
-    <li>Short names assigned to sequences retrieved from UniProt</li>
-    <li>Groovy console upgraded to 2.4.12 (improved support for Java 9)</li>
+    <li></li>
   </ul>
   <p>
     <strong><a name="experimental">Experimental Features</a></strong>
diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 3f5aa94..06c8b6b 100644
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -11,6 +11,7 @@ action.paste = Paste
 action.show_html_source = Show HTML Source
 action.print = Print...
 action.web_service = Web Service
+action.hmmer = HMMER
 action.cancel_job = Cancel Job
 action.start_job = Start Job
 action.revert = Revert
@@ -203,6 +204,8 @@ label.colourScheme_purine/pyrimidine = Purine/Pyrimidine
 label.colourScheme_nucleotide = Nucleotide
 label.colourScheme_t-coffee_scores = T-Coffee Scores
 label.colourScheme_rna_helices = By RNA Helices
+label.colourScheme_hmmer-uniprot = HMMER profile v global background
+label.colourScheme_hmmer-alignment = HMMER profile v alignment background
 label.blc = BLC
 label.fasta = Fasta
 label.msf = MSF
@@ -1147,6 +1150,9 @@ status.loading_cached_pdb_entries = Loading Cached PDB Entries
 status.searching_for_pdb_structures = Searching for PDB Structures
 status.opening_file_for = opening file for
 status.colouring_chimera = Colouring Chimera
+status.running_hmmbuild = Building Hidden Markov Model
+status.running_hmmalign = Creating alignment with Hidden Markov Model
+status.running_hmmsearch = Searching for matching sequences
 label.font_doesnt_have_letters_defined = Font doesn't have letters defined\nso cannot be used\nwith alignment data
 label.font_too_small = Font size is too small
 label.error_loading_file_params = Error loading file {0}
@@ -1367,3 +1373,65 @@ label.most_bound_molecules = Most Bound Molecules
 label.most_polymer_residues = Most Polymer Residues
 label.cached_structures = Cached Structures
 label.free_text_search = Free Text Search
+label.hmmalign = hmmalign
+label.hmmbuild = hmmbuild
+label.hmmbuild_group = Build HMM from Selected Group
+label.group_hmmbuild = Build HMM from Group
+label.hmmsearch = hmmsearch
+label.hmmer_location = HMMER Binaries Installation Location
+warn.null_hmm = Please ensure the alignment contains a hidden Markov model.
+label.ignore_below_background_frequency = Ignore Below Background Frequency
+label.information_description = Information content, measured in bits
+warn.no_selected_hmm = Please select a hidden Markov model sequence.
+label.select_hmm = Select HMM
+warn.no_sequence_data = No sequence data found.
+warn.empty_grp_or_alignment = An empty group or alignment was found.
+label.no_sequences_found = No matching sequences, or an error occurred.
+label.hmmer = HMMER
+label.trim_termini = Trim Non-Matching Termini
+label.trim_termini_desc = If true, non-matching regions on either end of the resulting alignment are removed.
+label.no_of_sequences = Sequences Returned
+label.freq_alignment = Use Alignment Background Frequencies
+label.freq_uniprot = Use Uniprot Background Frequencies
+label.hmmalign_label = hmmalign Options
+label.hmmsearch_label = hmmsearch Options
+label.hmmbuild_not_found = The hmmbuild binary was not found
+label.hmmalign_not_found = The hmmalign binary was not found
+label.hmmsearch_not_found = The hmmsearch binary was not found
+warn.hmm_command_failed = hmm command not found
+label.invalid_folder = Invalid Folder
+label.folder_not_exists = HMMER binaries not found. \n Please enter the path to the HMMER binaries (if installed).
+label.hmmer_installed = HMMER installed
+label.hmmer_no_sequences_found = No sequences found
+label.number_of_results = Number of Results to Return
+label.auto_align_seqs = Automatically Align Fetched Sequences
+label.use_accessions = Return Accessions
+label.seq_e_value = Sequence E-value Cutoff
+label.seq_score = Sequence Score Threshold
+label.dom_e_value = Domain E-value Cutoff
+label.dom_score = Domain Score Threshold
+label.number_of_results_desc = The maximum number of results that hmmsearch will return
+label.auto_align_seqs_desc = If true, all fetched sequences will be aligned to the hidden Markov model with which the search was performed
+label.use_accessions_desc = If true, the accession number of each sequence is returned, rather than that sequences name
+label.seq_e_value_desc = The E-value cutoff for returned sequences
+label.seq_score_desc = The score threshold for returned sequences
+label.dom_e_value_desc = The E-value cutoff for returned domains
+label.dom_score_desc = The score threshold for returned domains
+label.not_enough_sequences = There are not enough sequences to run {0}
+label.add_database = Add Database
+label.this_alignment = This alignment
+warn.file_not_exists = File does not exist
+warn.invalid_format = This is not a valid database file format. The current supported formats are Fasta, Stockholm and Pfam.
+label.database_for_hmmsearch = The database hmmsearch will search through
+label.use_reference = Use Reference Annotation
+label.use_reference_desc = If true, hmmbuild will keep all columns defined as a reference position by the reference annotation
+label.hmm_name = HMM Name
+label.hmm_name_desc = The name given to the HMM.
+warn.no_reference_annotation = No reference annotation found.
+label.hmmbuild_for = Build HMM for
+label.hmmbuild_for_desc = Build an HMM for the selected sequence groups.
+label.alignment = Alignment
+label.groups_and_alignment = All groups and alignment
+label.groups = All groups
+label.selected_group = Selected group
+label.use_info_for_height = Use Information Content as Letter Height
diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index f4bd31c..29b994e 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -162,6 +162,50 @@ public class PDBChain
   }
 
   /**
+   * Annotate the residues with their corresponding positions in s1 using the
+   * alignment in as NOTE: This clears all atom.alignmentMapping values on the
+   * structure.
+   * 
+   * @param as
+   * @param s1
+   */
+  public void makeExactMapping(StructureMapping mapping, SequenceI s1)
+  {
+    // first clear out any old alignmentMapping values:
+    for (Atom atom : atoms)
+    {
+      atom.alignmentMapping = -1;
+    }
+    SequenceI ds = s1;
+    while (ds.getDatasetSequence() != null)
+    {
+      ds = ds.getDatasetSequence();
+    }
+    int pdboffset = 0;
+    for (Residue res : residues)
+    {
+      // res.number isn't set correctly for discontinuous/mismapped residues
+      int seqpos = mapping.getSeqPos(res.atoms.get(0).resNumber);
+      char strchar = sequence.getCharAt(pdboffset++);
+      if (seqpos == StructureMapping.UNASSIGNED_VALUE)
+      {
+        continue;
+      }
+      char seqchar = ds.getCharAt(seqpos - ds.getStart());
+
+      boolean sameResidue = Comparison.isSameResidue(
+              seqchar, strchar, false);
+      if (sameResidue)
+      {
+        for (Atom atom : res.atoms)
+        {
+          atom.alignmentMapping = seqpos - 1;
+        }
+      }
+    }
+  }
+
+  /**
    * Copies over the RESNUM seqfeatures from the internal chain sequence to the
    * mapped sequence
    * 
@@ -550,6 +594,12 @@ public class PDBChain
   {
     SequenceI sq = mapping.getSequence();
     SequenceI dsq = sq;
+    if (sqmpping == null)
+    {
+      // SIFTS mappings are recorded in the StructureMapping object...
+
+      sqmpping = mapping.getSeqToPdbMapping();
+    }
     if (sq != null)
     {
       while (dsq.getDatasetSequence() != null)
diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index e4f2dfa..11c8f72 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -24,6 +24,7 @@ import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenMarkovModel;
 import jalview.datamodel.Profile;
 import jalview.datamodel.ProfileI;
 import jalview.datamodel.Profiles;
@@ -32,6 +33,7 @@ import jalview.datamodel.ResidueCount;
 import jalview.datamodel.ResidueCount.SymbolCounts;
 import jalview.datamodel.SequenceI;
 import jalview.ext.android.SparseIntArray;
+import jalview.schemes.ResidueProperties;
 import jalview.util.Comparison;
 import jalview.util.Format;
 import jalview.util.MappingUtils;
@@ -48,25 +50,12 @@ import java.util.List;
  * This class is used extensively in calculating alignment colourschemes that
  * depend on the amount of conservation in each alignment column.
  * 
- * @author $author$
- * @version $Revision$
  */
 public class AAFrequency
 {
-  public static final String PROFILE = "P";
-
-  /*
-   * Quick look-up of String value of char 'A' to 'Z'
-   */
-  private static final String[] CHARS = new String['Z' - 'A' + 1];
+  private static final double LOG2 = Math.log(2);
 
-  static
-  {
-    for (char c = 'A'; c <= 'Z'; c++)
-    {
-      CHARS[c - 'A'] = String.valueOf(c);
-    }
-  }
+  public static final String PROFILE = "P";
 
   public static final ProfilesI calculate(List<SequenceI> list, int start,
           int end)
@@ -192,6 +181,52 @@ public class AAFrequency
   }
 
   /**
+   * Returns the full set of profiles for a hidden Markov model. The underlying
+   * data is the raw probabilities of a residue being emitted at each node,
+   * however the profiles returned by this function contain the percentage
+   * chance of a residue emission.
+   * 
+   * @param hmm
+   * @param width
+   *          The width of the Profile array (Profiles) to be returned.
+   * @param start
+   *          The alignment column on which the first profile is based.
+   * @param end
+   *          The alignment column on which the last profile is based.
+   * @param removeBelowBackground
+   *          if true, symbols with a match emission probability less than
+   *          background frequency are ignored
+   * @return
+   */
+  public static ProfilesI calculateHMMProfiles(final HiddenMarkovModel hmm,
+          int width, int start, int end, boolean removeBelowBackground,
+          boolean infoLetterHeight)
+  {
+    ProfileI[] result = new ProfileI[width];
+    char[] symbols = hmm.getSymbols().toCharArray();
+    int symbolCount = symbols.length;
+    for (int column = start; column < end; column++)
+    {
+      ResidueCount counts = new ResidueCount();
+      for (char symbol : symbols)
+      {
+        int value = getAnalogueCount(hmm, column, symbol,
+                removeBelowBackground, infoLetterHeight);
+        counts.put(symbol, value);
+      }
+      int maxCount = counts.getModalCount();
+      String maxResidue = counts.getResiduesForCount(maxCount);
+      int gapCount = counts.getGapCount();
+      ProfileI profile = new Profile(symbolCount, gapCount, maxCount,
+              maxResidue);
+      profile.setCounts(counts);
+
+      result[column] = profile;
+    }
+    return new Profiles(result);
+  }
+
+  /**
    * Make an estimate of the profile size we are going to compute i.e. how many
    * different characters may be present in it. Overestimating has a cost of
    * using more memory than necessary. Underestimating has a cost of needing to
@@ -289,9 +324,80 @@ public class AAFrequency
   }
 
   /**
-   * Derive the gap count annotation row.
+   * Derive the information annotations to be added to the alignment for
+   * display. This does not recompute the raw data, but may be called on a
+   * change in display options, such as 'ignore below background frequency',
+   * which may in turn result in a change in the derived values.
    * 
-   * @param gaprow
+   * @param information
+   *          the annotation row to add annotations to
+   * @param profiles
+   *          the source information data
+   * @param startCol
+   *          start column (inclusive)
+   * @param endCol
+   *          end column (exclusive)
+   * @param ignoreGaps
+   *          if true, normalise residue percentages
+   * @param showSequenceLogo
+   *          if true include all information symbols, else just show modal
+   *          residue
+   */
+  public static float completeInformation(AlignmentAnnotation information,
+          ProfilesI profiles, int startCol, int endCol)
+  {
+    // long now = System.currentTimeMillis();
+    if (information == null || information.annotations == null)
+    {
+      /*
+       * called with a bad alignment annotation row 
+       * wait for it to be initialised properly
+       */
+      return 0;
+    }
+
+    float max = 0f;
+    SequenceI hmmSeq = information.sequenceRef;
+
+    int seqLength = hmmSeq.getLength();
+    if (information.annotations.length < seqLength)
+    {
+      return 0;
+    }
+
+    HiddenMarkovModel hmm = hmmSeq.getHMM();
+
+    for (int column = startCol; column < endCol; column++)
+    {
+      if (column >= seqLength)
+      {
+        // hmm consensus sequence is shorter than the alignment
+        break;
+      }
+      
+      float value = hmm.getInformationContent(column);
+      boolean isNaN = Float.isNaN(value);
+      if (!isNaN)
+      {
+        max = Math.max(max, value);
+      }
+
+      String description = isNaN ? null
+              : String.format("%.4f bits", value);
+      information.annotations[column] = new Annotation(
+              Character.toString(
+                      Character.toUpperCase(hmmSeq.getCharAt(column))),
+              description, ' ', value);
+    }
+
+    information.graphMax = max;
+    return max;
+  }
+
+  /**
+   * Derive the occupancy count annotation
+   * 
+   * @param occupancy
    *          the annotation row to add annotations to
    * @param profiles
    *          the source consensus data
@@ -300,11 +406,11 @@ public class AAFrequency
    * @param endCol
    *          end column (exclusive)
    */
-  public static void completeGapAnnot(AlignmentAnnotation gaprow,
+  public static void completeOccupancyAnnot(AlignmentAnnotation occupancy,
           ProfilesI profiles, int startCol, int endCol, long nseq)
   {
-    if (gaprow == null || gaprow.annotations == null
-            || gaprow.annotations.length < endCol)
+    if (occupancy == null || occupancy.annotations == null
+            || occupancy.annotations.length < endCol)
     {
       /*
        * called with a bad alignment annotation row 
@@ -313,8 +419,8 @@ public class AAFrequency
       return;
     }
     // always set ranges again
-    gaprow.graphMax = nseq;
-    gaprow.graphMin = 0;
+    occupancy.graphMax = nseq;
+    occupancy.graphMin = 0;
     double scale = 0.8 / nseq;
     for (int i = startCol; i < endCol; i++)
     {
@@ -325,7 +431,7 @@ public class AAFrequency
          * happens if sequences calculated over were 
          * shorter than alignment width
          */
-        gaprow.annotations[i] = null;
+        occupancy.annotations[i] = null;
         return;
       }
 
@@ -333,7 +439,8 @@ public class AAFrequency
 
       String description = "" + gapped;
 
-      gaprow.annotations[i] = new Annotation("", description, '\0', gapped,
+      occupancy.annotations[i] = new Annotation("", description, '\0',
+              gapped,
               jalview.util.ColorUtils.bleachColour(Color.DARK_GRAY,
                       (float) scale * gapped));
     }
@@ -449,6 +556,7 @@ public class AAFrequency
     return result;
   }
 
+
   /**
    * Extract a sorted extract of cDNA codon profile data. The returned array
    * contains
@@ -531,7 +639,7 @@ public class AAFrequency
     for (int col = 0; col < cols; col++)
     {
       // todo would prefer a Java bean for consensus data
-      Hashtable<String, int[]> columnHash = new Hashtable<String, int[]>();
+      Hashtable<String, int[]> columnHash = new Hashtable<>();
       // #seqs, #ungapped seqs, counts indexed by (codon encoded + 1)
       int[] codonCounts = new int[66];
       codonCounts[0] = alignment.getSequences().size();
@@ -718,4 +826,118 @@ public class AAFrequency
     }
     return scale;
   }
+
+  /**
+   * Returns the sorted HMM profile for the given column of the alignment. The
+   * returned array contains
+   * 
+   * <pre>
+   *    [profileType=0, numberOfValues, 100, charValue1, percentage1, charValue2, percentage2, ...]
+   * in descending order of percentage value
+   * </pre>
+   * 
+   * @param hmm
+   * @param column
+   * @param removeBelowBackground
+   *          if true, ignores residues with probability less than their
+   *          background frequency
+   * @param infoHeight
+   *          if true, uses the log ratio 'information' measure to scale the
+   *          value
+   * @return
+   */
+  public static int[] extractHMMProfile(HiddenMarkovModel hmm, int column,
+          boolean removeBelowBackground, boolean infoHeight)
+  {
+    if (hmm == null)
+    {
+      return null;
+    }
+    String alphabet = hmm.getSymbols();
+    int size = alphabet.length();
+    char symbols[] = new char[size];
+    int values[] = new int[size];
+    int totalCount = 0;
+
+    for (int i = 0; i < size; i++)
+    {
+      char symbol = alphabet.charAt(i);
+      symbols[i] = symbol;
+      int value = getAnalogueCount(hmm, column, symbol,
+              removeBelowBackground, infoHeight);
+      values[i] = value;
+      totalCount += value;
+    }
+
+    /*
+     * sort symbols by increasing emission probability
+     */
+    QuickSort.sort(values, symbols);
+
+    int[] profile = new int[3 + size * 2];
+
+    profile[0] = AlignmentAnnotation.SEQUENCE_PROFILE;
+    profile[1] = size;
+    profile[2] = 100;
+
+    /*
+     * order symbol/count profile by decreasing emission probability
+     */
+    if (totalCount != 0)
+    {
+      int arrayPos = 3;
+      for (int k = size - 1; k >= 0; k--)
+      {
+        Float percentage;
+        int value = values[k];
+        if (removeBelowBackground)
+        {
+          percentage = ((float) value) / totalCount * 100f;
+        }
+        else
+        {
+          percentage = value / 100f;
+        }
+        int intPercent = Math.round(percentage);
+        profile[arrayPos] = symbols[k];
+        profile[arrayPos + 1] = intPercent;
+        arrayPos += 2;
+      }
+    }
+    return profile;
+  }
+
+  /**
+   * Converts the emission probability of a residue at a column in the alignment
+   * to a 'count', suitable for rendering as an annotation value
+   * 
+   * @param hmm
+   * @param column
+   * @param symbol
+   * @param removeBelowBackground
+   *          if true, returns 0 for any symbol with a match emission
+   *          probability less than the background frequency
+   * @infoHeight if true, uses the log ratio 'information content' to scale the
+   *             value
+   * @return
+   */
+  static int getAnalogueCount(HiddenMarkovModel hmm, int column,
+          char symbol, boolean removeBelowBackground, boolean infoHeight)
+  {
+    double value = hmm.getMatchEmissionProbability(column, symbol);
+    double freq = ResidueProperties.backgroundFrequencies
+            .get(hmm.getAlphabetType()).get(symbol);
+    if (value < freq && removeBelowBackground)
+    {
+      return 0;
+    }
+
+    if (infoHeight)
+    {
+      value = value * (Math.log(value / freq) / LOG2);
+    }
+
+    value = value * 10000d;
+    return Math.round((float) value);
+  }
 }
diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 5e11446..d1217bf 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -1888,7 +1888,7 @@ public class AlignmentUtils
    * @param seqMappings
    *          the set of mappings involving dnaSeq
    * @param aMapping
-   *          an initial candidate from seqMappings
+   *          a transcript-to-peptide mapping
    * @return
    */
   static SequenceI findCdsForProtein(List<AlignedCodonFrame> mappings,
@@ -1913,7 +1913,15 @@ public class AlignmentUtils
     if (mappedFromLength == dnaLength
             || mappedFromLength == dnaLength - CODON_LENGTH)
     {
-      return seqDss;
+      /*
+       * if sequence has CDS features, this is a transcript with no UTR
+       * - do not take this as the CDS sequence! (JAL-2789)
+       */
+      if (seqDss.getFeatures().getFeaturesByOntology(SequenceOntologyI.CDS)
+              .isEmpty())
+      {
+        return seqDss;
+      }
     }
 
     /*
@@ -1938,10 +1946,12 @@ public class AlignmentUtils
           {
             /*
             * found a 3:1 mapping to the protein product which covers
-            * the whole dna sequence i.e. is from CDS; finally check it
-            * is from the dna start sequence
+            * the whole dna sequence i.e. is from CDS; finally check the CDS
+            * is mapped from the given dna start sequence
             */
             SequenceI cdsSeq = map.getFromSeq();
+            // todo this test is weak if seqMappings contains multiple mappings;
+            // we get away with it if transcript:cds relationship is 1:1
             List<AlignedCodonFrame> dnaToCdsMaps = MappingUtils
                     .findMappingsForSequence(cdsSeq, seqMappings);
             if (!dnaToCdsMaps.isEmpty())
@@ -2056,9 +2066,11 @@ public class AlignmentUtils
   protected static List<DBRefEntry> propagateDBRefsToCDS(SequenceI cdsSeq,
           SequenceI contig, SequenceI proteinProduct, Mapping mapping)
   {
+
     // gather direct refs from contig congruent with mapping
     List<DBRefEntry> direct = new ArrayList<>();
     HashSet<String> directSources = new HashSet<>();
+
     if (contig.getDBRefs() != null)
     {
       for (DBRefEntry dbr : contig.getDBRefs())
@@ -2235,12 +2247,13 @@ public class AlignmentUtils
     int mappedDnaLength = MappingUtils.getLength(ranges);
 
     /*
-     * if not a whole number of codons, something is wrong,
-     * abort mapping
+     * if not a whole number of codons, truncate mapping
      */
-    if (mappedDnaLength % CODON_LENGTH > 0)
+    int codonRemainder = mappedDnaLength % CODON_LENGTH;
+    if (codonRemainder > 0)
     {
-      return null;
+      mappedDnaLength -= codonRemainder;
+      MappingUtils.removeEndPositions(codonRemainder, ranges);
     }
 
     int proteinLength = proteinSeq.getLength();
diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index ef05a58..2ad8487 100644
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -44,6 +44,7 @@ import jalview.util.ShiftList;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Comparator;
+import java.util.Iterator;
 import java.util.List;
 
 public class Dna
@@ -56,19 +57,23 @@ public class Dna
    * 'final' variables describe the inputs to the translation, which should not
    * be modified.
    */
-  final private List<SequenceI> selection;
+  private final List<SequenceI> selection;
 
-  final private String[] seqstring;
+  private final String[] seqstring;
 
-  final private int[] contigs;
+  private final Iterator<int[]> contigs;
 
-  final private char gapChar;
+  private final char gapChar;
 
-  final private AlignmentAnnotation[] annotations;
+  private final AlignmentAnnotation[] annotations;
 
-  final private int dnaWidth;
+  private final int dnaWidth;
 
-  final private AlignmentI dataset;
+  private final AlignmentI dataset;
+
+  private ShiftList vismapping;
+
+  private int[] startcontigs;
 
   /*
    * Working variables for the translation.
@@ -91,7 +96,7 @@ public class Dna
    * @param viewport
    * @param visibleContigs
    */
-  public Dna(AlignViewportI viewport, int[] visibleContigs)
+  public Dna(AlignViewportI viewport, Iterator<int[]> visibleContigs)
   {
     this.selection = Arrays.asList(viewport.getSequenceSelection());
     this.seqstring = viewport.getViewAsString(true);
@@ -100,6 +105,45 @@ public class Dna
     this.annotations = viewport.getAlignment().getAlignmentAnnotation();
     this.dnaWidth = viewport.getAlignment().getWidth();
     this.dataset = viewport.getAlignment().getDataset();
+    initContigs();
+  }
+
+  /**
+   * Initialise contigs used as starting point for translateCodingRegion
+   */
+  private void initContigs()
+  {
+    vismapping = new ShiftList(); // map from viscontigs to seqstring
+    // intervals
+
+    int npos = 0;
+    int[] lastregion = null;
+    ArrayList<Integer> tempcontigs = new ArrayList<>();
+    while (contigs.hasNext())
+    {
+      int[] region = contigs.next();
+      if (lastregion == null)
+      {
+        vismapping.addShift(npos, region[0]);
+      }
+      else
+      {
+        // hidden region
+        vismapping.addShift(npos, region[0] - lastregion[1] + 1);
+      }
+      lastregion = region;
+      tempcontigs.add(region[0]);
+      tempcontigs.add(region[1]);
+    }
+
+    startcontigs = new int[tempcontigs.size()];
+    int i = 0;
+    for (Integer val : tempcontigs)
+    {
+      startcontigs[i] = val;
+      i++;
+    }
+    tempcontigs = null;
   }
 
   /**
@@ -392,26 +436,13 @@ public class Dna
           List<SequenceI> proteinSeqs)
   {
     List<int[]> skip = new ArrayList<>();
-    int skipint[] = null;
-    ShiftList vismapping = new ShiftList(); // map from viscontigs to seqstring
-    // intervals
-    int vc;
-    int[] scontigs = new int[contigs.length];
+    int[] skipint = null;
+
     int npos = 0;
-    for (vc = 0; vc < contigs.length; vc += 2)
-    {
-      if (vc == 0)
-      {
-        vismapping.addShift(npos, contigs[vc]);
-      }
-      else
-      {
-        // hidden region
-        vismapping.addShift(npos, contigs[vc] - contigs[vc - 1] + 1);
-      }
-      scontigs[vc] = contigs[vc];
-      scontigs[vc + 1] = contigs[vc + 1];
-    }
+    int vc = 0;
+
+    int[] scontigs = new int[startcontigs.length];
+    System.arraycopy(startcontigs, 0, scontigs, 0, startcontigs.length);
 
     // allocate a roughly sized buffer for the protein sequence
     StringBuilder protein = new StringBuilder(seqstring.length() / 2);
diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index fabd0c6..2c077b6 100755
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -20,6 +20,7 @@
  */
 package jalview.analysis;
 
+import jalview.datamodel.HiddenMarkovModel;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
@@ -35,7 +36,7 @@ public class SeqsetUtils
 
   /**
    * Store essential properties of a sequence in a hashtable for later recovery
-   * Keys are Name, Start, End, SeqFeatures, PdbId
+   * Keys are Name, Start, End, SeqFeatures, PdbId, HMM
    * 
    * @param seq
    *          SequenceI
@@ -69,6 +70,10 @@ public class SeqsetUtils
               (seq.getDatasetSequence() != null) ? seq.getDatasetSequence()
                       : new Sequence("THISISAPLACEHOLDER", ""));
     }
+    if (seq.isHMMConsensusSequence())
+    {
+      sqinfo.put("HMM", seq.getHMM());
+    }
     return sqinfo;
   }
 
@@ -97,6 +102,7 @@ public class SeqsetUtils
     Vector<PDBEntry> pdbid = (Vector<PDBEntry>) sqinfo.get("PdbId");
     String description = (String) sqinfo.get("Description");
     Sequence seqds = (Sequence) sqinfo.get("datasetSequence");
+    HiddenMarkovModel hmm = (HiddenMarkovModel) sqinfo.get("HMM");
     if (oldname == null)
     {
       namePresent = false;
@@ -135,6 +141,11 @@ public class SeqsetUtils
       sq.setDatasetSequence(seqds);
     }
 
+    if (hmm != null)
+    {
+      sq.setHMM(new HiddenMarkovModel(hmm));
+      sq.setIsHMMConsensusSequence(true);
+    }
     return namePresent;
   }
 
diff --git a/src/jalview/api/AlignCalcWorkerI.java b/src/jalview/api/AlignCalcWorkerI.java
index 85157c4..1387cba 100644
--- a/src/jalview/api/AlignCalcWorkerI.java
+++ b/src/jalview/api/AlignCalcWorkerI.java
@@ -39,8 +39,8 @@ public interface AlignCalcWorkerI extends Runnable
 
   /**
    * Updates the display of calculated annotation values (does not recalculate
-   * the values). This allows ßquick redraw of annotations when display settings
-   * are changed.
+   * the values). This allows a quick redraw of annotations when display
+   * settings are changed.
    */
   void updateAnnotation();
 
diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 931eba6..6b3cbe8 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -54,7 +54,7 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @return
    */
-  public ViewportRanges getRanges();
+  ViewportRanges getRanges();
 
   /**
    * calculate the height for visible annotation, revalidating bounds where
@@ -62,7 +62,7 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @return total height of annotation
    */
-  public int calcPanelHeight();
+  int calcPanelHeight();
 
   /**
    * Answers true if the viewport has at least one column selected
@@ -86,6 +86,12 @@ public interface AlignViewportI extends ViewStyleI
 
   boolean isNormaliseSequenceLogo();
 
+  boolean isShowInformationHistogram();
+
+  boolean isShowHMMSequenceLogo();
+
+  boolean isNormaliseHMMSequenceLogo();
+
   ColourSchemeI getGlobalColourScheme();
 
   /**
@@ -100,7 +106,7 @@ public interface AlignViewportI extends ViewStyleI
 
   ColumnSelection getColumnSelection();
 
-  ProfilesI getSequenceConsensusHash();
+  ProfilesI getConsensusProfiles();
 
   /**
    * Get consensus data table for the cDNA complement of this alignment (if any)
@@ -113,6 +119,8 @@ public interface AlignViewportI extends ViewStyleI
 
   boolean isIgnoreGapsConsensus();
 
+  boolean isIgnoreBelowBackground();
+
   boolean isCalculationInProgress(AlignmentAnnotation alignmentAnnotation);
 
   AlignmentAnnotation getAlignmentQualityAnnot();
@@ -131,7 +139,7 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @return
    */
-  AlignmentAnnotation getAlignmentGapAnnotation();
+  AlignmentAnnotation getOccupancyAnnotation();
 
   /**
    * get the container for cDNA complement consensus annotation
@@ -170,7 +178,7 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @param hconsensus
    */
-  void setSequenceConsensusHash(ProfilesI hconsensus);
+  void setConsensusProfiles(ProfilesI hconsensus);
 
   /**
    * Set the cDNA complement consensus for the viewport
@@ -380,14 +388,14 @@ public interface AlignViewportI extends ViewStyleI
    * 
    * @return a copy of this view's current display settings
    */
-  public ViewStyleI getViewStyle();
+  ViewStyleI getViewStyle();
 
   /**
    * update the view's display settings with the given style set
    * 
    * @param settingsForView
    */
-  public void setViewStyle(ViewStyleI settingsForView);
+  void setViewStyle(ViewStyleI settingsForView);
 
   /**
    * Returns a viewport which holds the cDna for this (protein), or vice versa,
@@ -431,7 +439,7 @@ public interface AlignViewportI extends ViewStyleI
    */
   void setFollowHighlight(boolean b);
 
-  public void applyFeaturesStyle(FeatureSettingsModelI featureSettings);
+  void applyFeaturesStyle(FeatureSettingsModelI featureSettings);
 
   /**
    * check if current selection group is defined on the view, or is simply a
@@ -487,7 +495,21 @@ public interface AlignViewportI extends ViewStyleI
   @Override
   void setProteinFontAsCdna(boolean b);
 
-  public abstract TreeModel getCurrentTree();
+  void setHmmProfiles(ProfilesI info);
+
+  ProfilesI getHmmProfiles();
+
+  /**
+   * Registers and starts a worker thread to calculate Information Content
+   * annotation, if it is not already registered
+   * 
+   * @param ap
+   */
+  void initInformationWorker(AlignmentViewPanel ap);
+
+  boolean isInfoLetterHeight();
+
+  abstract TreeModel getCurrentTree();
 
-  public abstract void setCurrentTree(TreeModel tree);
+  abstract void setCurrentTree(TreeModel tree);
 }
diff --git a/src/jalview/api/structures/JalviewStructureDisplayI.java b/src/jalview/api/structures/JalviewStructureDisplayI.java
index fd66388..b4612cf 100644
--- a/src/jalview/api/structures/JalviewStructureDisplayI.java
+++ b/src/jalview/api/structures/JalviewStructureDisplayI.java
@@ -62,4 +62,11 @@ public interface JalviewStructureDisplayI
    */
   void setJalviewColourScheme(ColourSchemeI colourScheme);
 
+  /**
+   * 
+   * @return true if all background sequence/structure binding threads have
+   *         completed for this viewer instance
+   */
+  boolean hasMapping();
+
 }
diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index fe6b8d9..28aabe1 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -234,6 +234,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
             alignPanel);
     viewport.updateConservation(alignPanel);
     viewport.updateConsensus(alignPanel);
+    viewport.initInformationWorker(alignPanel);
 
     displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
     followMouseOverFlag.setState(viewport.isFollowHighlight());
@@ -1906,7 +1907,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   static StringBuffer copiedSequences;
 
-  static Vector<int[]> copiedHiddenColumns;
+  static HiddenColumns copiedHiddenColumns;
 
   protected void copy_actionPerformed()
   {
@@ -1930,14 +1931,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
     if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
     {
-      copiedHiddenColumns = new Vector<>(viewport.getAlignment()
-              .getHiddenColumns().getHiddenColumnsCopy());
       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
-      for (int[] region : copiedHiddenColumns)
-      {
-        region[0] = region[0] - hiddenOffset;
-        region[1] = region[1] - hiddenOffset;
-      }
+      int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
+
+      // create new HiddenColumns object with copy of hidden regions
+      // between startRes and endRes, offset by startRes
+      copiedHiddenColumns = new HiddenColumns(
+              viewport.getAlignment().getHiddenColumns(), hiddenOffset,
+              hiddenCutoff, hiddenOffset);
     }
     else
     {
@@ -2006,13 +2007,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   {
     try
     {
-
       if (copiedSequences == null)
       {
         return;
       }
 
-      StringTokenizer st = new StringTokenizer(copiedSequences.toString());
+      StringTokenizer st = new StringTokenizer(copiedSequences.toString(),
+              "\t");
       Vector seqs = new Vector();
       while (st.hasMoreElements())
       {
@@ -2044,14 +2045,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         }
         AlignFrame af = new AlignFrame(new Alignment(newSeqs),
                 viewport.applet, newtitle, false);
-        if (copiedHiddenColumns != null)
-        {
-          for (int i = 0; i < copiedHiddenColumns.size(); i++)
-          {
-            int[] region = copiedHiddenColumns.elementAt(i);
-            af.viewport.hideColumns(region[0], region[1]);
-          }
-        }
+        af.viewport.setHiddenColumns(copiedHiddenColumns);
 
         jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
                 frameHeight);
diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 262948d..753e972 100644
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
  * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
  * 
  * This file is part of Jalview.
  * 
@@ -25,14 +25,11 @@ import jalview.api.FeatureSettingsModelI;
 import jalview.bin.JalviewLite;
 import jalview.commands.CommandI;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SearchResultsI;
-import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
 import jalview.renderer.ResidueShader;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.schemes.UserColourScheme;
@@ -59,6 +56,12 @@ public class AlignViewport extends AlignmentViewport
 
   private AnnotationColumnChooser annotationColumnSelectionState;
 
+  java.awt.Frame nullFrame;
+
+  protected FeatureSettings featureSettings = null;
+
+  private float heightScale = 1, widthScale = 1;
+
   public AlignViewport(AlignmentI al, JalviewLite applet)
   {
     super(al);
@@ -200,10 +203,11 @@ public class AlignViewport extends AlignmentViewport
       if (colour != null)
       {
         residueShading = new ResidueShader(
-                ColourSchemeProperty.getColourScheme(alignment, colour));
+                ColourSchemeProperty.getColourScheme(getAlignment(),
+                        colour));
         if (residueShading != null)
         {
-          residueShading.setConsensus(hconsensus);
+          residueShading.setConsensus(consensusProfiles);
         }
       }
 
@@ -214,15 +218,8 @@ public class AlignViewport extends AlignmentViewport
       }
     }
     initAutoAnnotation();
-
   }
 
-  java.awt.Frame nullFrame;
-
-  protected FeatureSettings featureSettings = null;
-
-  private float heightScale = 1, widthScale = 1;
-
   /**
    * {@inheritDoc}
    */
@@ -302,17 +299,6 @@ public class AlignViewport extends AlignmentViewport
             .getStructureSelectionManager(applet);
   }
 
-  @Override
-  public boolean isNormaliseSequenceLogo()
-  {
-    return normaliseSequenceLogo;
-  }
-
-  public void setNormaliseSequenceLogo(boolean state)
-  {
-    normaliseSequenceLogo = state;
-  }
-
   /**
    * 
    * @return true if alignment characters should be displayed
diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index 270b2f7..730434f 100644
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -421,8 +421,8 @@ public class AlignmentPanel extends Panel
     if (av.hasHiddenColumns())
     {
       AlignmentI al = av.getAlignment();
-      start = al.getHiddenColumns().findColumnPosition(ostart);
-      end = al.getHiddenColumns().findColumnPosition(end);
+      start = al.getHiddenColumns().absoluteToVisibleColumn(ostart);
+      end = al.getHiddenColumns().absoluteToVisibleColumn(end);
       if (start == end)
       {
         if (!scrollToNearest && !al.getHiddenColumns().isVisible(ostart))
@@ -554,8 +554,8 @@ public class AlignmentPanel extends Panel
     // this is called after loading new annotation onto alignment
     if (alignFrame.getSize().height == 0)
     {
-      System.out.println(
-              "adjustAnnotationHeight frame size zero NEEDS FIXING");
+      // panel not laid out yet?
+      return;
     }
     fontChanged();
     validateAnnotationDimensions(true);
@@ -675,7 +675,7 @@ public class AlignmentPanel extends Panel
       if (av.hasHiddenColumns())
       {
         width = av.getAlignment().getHiddenColumns()
-                .findColumnPosition(width);
+                .absoluteToVisibleColumn(width);
       }
       if (x < 0)
       {
diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index c049326..71dc3da 100755
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -23,6 +23,7 @@ package jalview.appletgui;
 import jalview.analysis.AlignmentUtils;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.util.MessageManager;
@@ -51,13 +52,22 @@ import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
 import java.util.Arrays;
 import java.util.Collections;
-import java.util.Vector;
 
 public class AnnotationLabels extends Panel
         implements ActionListener, MouseListener, MouseMotionListener
 {
   Image image;
 
+  /**
+   * width in pixels within which height adjuster arrows are shown and active
+   */
+  private static final int HEIGHT_ADJUSTER_WIDTH = 50;
+
+  /**
+   * height in pixels for allowing height adjuster to be active
+   */
+  private static int HEIGHT_ADJUSTER_HEIGHT = 10;
+
   boolean active = false;
 
   AlignmentPanel ap;
@@ -93,23 +103,6 @@ public class AnnotationLabels extends Panel
     this.ap = ap;
     this.av = ap.av;
     setLayout(null);
-
-    /**
-     * this retrieves the adjustable height glyph from resources. we don't use
-     * it at the moment. java.net.URL url =
-     * getClass().getResource("/images/idwidth.gif"); Image temp = null;
-     * 
-     * if (url != null) { temp =
-     * java.awt.Toolkit.getDefaultToolkit().createImage(url); }
-     * 
-     * try { MediaTracker mt = new MediaTracker(this); mt.addImage(temp, 0);
-     * mt.waitForID(0); } catch (Exception ex) { }
-     * 
-     * BufferedImage bi = new BufferedImage(temp.getHeight(this),
-     * temp.getWidth(this), BufferedImage.TYPE_INT_RGB); Graphics2D g =
-     * (Graphics2D) bi.getGraphics(); g.rotate(Math.toRadians(90));
-     * g.drawImage(temp, 0, -bi.getWidth(this), this); image = (Image) bi;
-     */
     addMouseListener(this);
     addMouseMotionListener(this);
   }
@@ -209,7 +202,9 @@ public class AnnotationLabels extends Panel
     }
     else if (evt.getActionCommand().equals(COPYCONS_SEQ))
     {
-      SequenceI cons = av.getConsensusSeq();
+      SequenceGroup group = aa[selectedRow].groupRef;
+      SequenceI cons = group == null ? av.getConsensusSeq()
+              : group.getConsensusSeq();
       if (cons != null)
       {
         copy_annotseqtoclipboard(cons);
@@ -269,7 +264,8 @@ public class AnnotationLabels extends Panel
   @Override
   public void mouseMoved(MouseEvent evt)
   {
-    resizePanel = evt.getY() < 10 && evt.getX() < 14;
+    resizePanel = evt.getY() < HEIGHT_ADJUSTER_HEIGHT
+            && evt.getX() < HEIGHT_ADJUSTER_WIDTH;
     setCursor(Cursor.getPredefinedCursor(
             resizePanel ? Cursor.S_RESIZE_CURSOR : Cursor.DEFAULT_CURSOR));
     int row = getSelectedRow(evt.getY() + scrollOffset);
@@ -538,7 +534,7 @@ public class AnnotationLabels extends Panel
                     MessageManager.getString("label.ignore_gaps_consensus"),
                     (aa[selectedRow].groupRef != null)
                             ? aa[selectedRow].groupRef
-                                    .getIgnoreGapsConsensus()
+                                    .isIgnoreGapsConsensus()
                             : ap.av.isIgnoreGapsConsensus());
             final AlignmentAnnotation aaa = aa[selectedRow];
             cbmi.addItemListener(new ItemListener()
@@ -849,8 +845,8 @@ public class AnnotationLabels extends Panel
                     + "\t" + sq.getSequenceAsString() + "\n");
     if (av.hasHiddenColumns())
     {
-      jalview.appletgui.AlignFrame.copiedHiddenColumns = new Vector<>(
-              av.getAlignment().getHiddenColumns().getHiddenColumnsCopy());
+      jalview.appletgui.AlignFrame.copiedHiddenColumns = new HiddenColumns(
+              av.getAlignment().getHiddenColumns());
     }
   }
 
@@ -909,14 +905,8 @@ public class AnnotationLabels extends Panel
       }
     }
     g.translate(0, +scrollOffset);
-    if (resizePanel)
-    {
-      // g.setColor(Color.red);
-      // g.setPaintMode();
-      // g.drawLine(2, 8, 5, 2);
-      // g.drawLine(5, 2, 8, 8);
-    }
-    else if (!dragCancelled && dragEvent != null && aa != null)
+
+    if (!resizePanel && !dragCancelled && dragEvent != null && aa != null)
     {
       g.setColor(Color.lightGray);
       g.drawString(aa[selectedRow].label, dragEvent.getX(),
diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index 50a9e33..50bc184 100755
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -480,7 +480,7 @@ public class AnnotationPanel extends Panel
     if (av.hasHiddenColumns())
     {
       column = av.getAlignment().getHiddenColumns()
-              .adjustForHiddenColumns(column);
+              .visibleToAbsoluteColumn(column);
     }
 
     if (row > -1 && column < aa[row].annotations.length
diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java
index ad04171..a60aacd 100755
--- a/src/jalview/appletgui/FeatureSettings.java
+++ b/src/jalview/appletgui/FeatureSettings.java
@@ -66,7 +66,7 @@ import java.util.Set;
 
 public class FeatureSettings extends Panel
         implements ItemListener, MouseListener, MouseMotionListener,
-        ActionListener, AdjustmentListener, FeatureSettingsControllerI
+        AdjustmentListener, FeatureSettingsControllerI
 {
   FeatureRenderer fr;
 
@@ -121,8 +121,17 @@ public class FeatureSettings extends Panel
       add(scrollPane, BorderLayout.CENTER);
     }
 
-    Button invert = new Button("Invert Selection");
-    invert.addActionListener(this);
+    Button invert = new Button(
+            MessageManager.getString("label.invert_selection"));
+    invert.addActionListener(new ActionListener()
+    {
+
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        invertSelection();
+      }
+    });
 
     Panel lowerPanel = new Panel(new GridLayout(2, 1, 5, 10));
     lowerPanel.add(invert);
@@ -546,8 +555,7 @@ public class FeatureSettings extends Panel
     }
   }
 
-  @Override
-  public void actionPerformed(ActionEvent evt)
+  protected void invertSelection()
   {
     for (int i = 0; i < featurePanel.getComponentCount(); i++)
     {
diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java
index f5ea12e..296f898 100755
--- a/src/jalview/appletgui/IdCanvas.java
+++ b/src/jalview/appletgui/IdCanvas.java
@@ -286,7 +286,7 @@ public class IdCanvas extends Panel implements ViewportListenerI
     if (av.hasHiddenColumns())
     {
       maxwidth = av.getAlignment().getHiddenColumns()
-              .findColumnPosition(maxwidth) - 1;
+              .absoluteToVisibleColumn(maxwidth) - 1;
     }
 
     int annotationHeight = 0;
diff --git a/src/jalview/appletgui/IdwidthAdjuster.java b/src/jalview/appletgui/IdwidthAdjuster.java
index e9722fe..2602268 100755
--- a/src/jalview/appletgui/IdwidthAdjuster.java
+++ b/src/jalview/appletgui/IdwidthAdjuster.java
@@ -20,10 +20,9 @@
  */
 package jalview.appletgui;
 
+import java.awt.Color;
 import java.awt.Cursor;
 import java.awt.Dimension;
-import java.awt.Graphics;
-import java.awt.Image;
 import java.awt.Panel;
 import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
@@ -36,20 +35,13 @@ public class IdwidthAdjuster extends Panel
 
   int oldX = 0;
 
-  Image image;
-
   AlignmentPanel ap;
 
   public IdwidthAdjuster(AlignmentPanel ap)
   {
     setLayout(null);
     this.ap = ap;
-    java.net.URL url = getClass().getResource("/images/idwidth.gif");
-    if (url != null)
-    {
-      image = java.awt.Toolkit.getDefaultToolkit().getImage(url);
-    }
-
+    setBackground(Color.WHITE);
     addMouseListener(this);
     addMouseMotionListener(this);
   }
@@ -129,19 +121,4 @@ public class IdwidthAdjuster extends Panel
   public void mouseClicked(MouseEvent evt)
   {
   }
-
-  @Override
-  public void paint(Graphics g)
-  {
-    // g.setColor(Color.white);
-    // g.fillRect(0, 0, getSize().width, getSize().height);
-    // if (active)
-    // {
-    // if (image != null)
-    // {
-    // g.drawImage(image, getSize().width - 20, 2, this);
-    // }
-    // }
-  }
-
 }
diff --git a/src/jalview/appletgui/OverviewCanvas.java b/src/jalview/appletgui/OverviewCanvas.java
index 9597b44..ecc90b8 100644
--- a/src/jalview/appletgui/OverviewCanvas.java
+++ b/src/jalview/appletgui/OverviewCanvas.java
@@ -132,7 +132,6 @@ public class OverviewCanvas extends Component
               od.getColumns(av.getAlignment()));
       mg.translate(0, -od.getSequencesHeight());
     }
-    System.gc();
 
     if (restart)
     {
diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 8ce597d..e09280f 100755
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -69,7 +69,7 @@ public class OverviewPanel extends Panel implements Runnable,
 
     od = new OverviewDimensionsShowHidden(av.getRanges(),
             (av.isShowAnnotation()
-                    && av.getSequenceConsensusHash() != null));
+                    && av.getConsensusProfiles() != null));
 
     oviewCanvas = new OverviewCanvas(od, av);
     setLayout(new BorderLayout());
@@ -155,6 +155,10 @@ public class OverviewPanel extends Panel implements Runnable,
       if (!od.isPositionInBox(evt.getX(), evt.getY()))
       { 
     	draggingBox = false;
+
+        // display drag cursor at mouse position
+        setCursor(Cursor.getPredefinedCursor(Cursor.MOVE_CURSOR));
+
         od.updateViewportFromMouse(evt.getX(), evt.getY(),
                 av.getAlignment().getHiddenSequences(),
                 av.getAlignment().getHiddenColumns());
@@ -172,6 +176,7 @@ public class OverviewPanel extends Panel implements Runnable,
   @Override
   public void mouseReleased(MouseEvent evt)
   {
+    draggingBox = false;
   }
 
   @Override
diff --git a/src/jalview/appletgui/ScalePanel.java b/src/jalview/appletgui/ScalePanel.java
index 04fb22b..c91449f 100755
--- a/src/jalview/appletgui/ScalePanel.java
+++ b/src/jalview/appletgui/ScalePanel.java
@@ -42,6 +42,7 @@ import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
 import java.beans.PropertyChangeEvent;
+import java.util.Iterator;
 import java.util.List;
 
 public class ScalePanel extends Panel
@@ -86,7 +87,7 @@ public class ScalePanel extends Panel
 
     if (av.hasHiddenColumns())
     {
-      res = av.getAlignment().getHiddenColumns().adjustForHiddenColumns(x);
+      res = av.getAlignment().getHiddenColumns().visibleToAbsoluteColumn(x);
     }
     else
     {
@@ -173,7 +174,7 @@ public class ScalePanel extends Panel
       });
       pop.add(item);
 
-      if (av.getAlignment().getHiddenColumns().hasManyHiddenColumns())
+      if (av.getAlignment().getHiddenColumns().hasMultiHiddenColumnRegions())
       {
         item = new MenuItem(MessageManager.getString("action.reveal_all"));
         item.addActionListener(new ActionListener()
@@ -234,7 +235,7 @@ public class ScalePanel extends Panel
     if (av.hasHiddenColumns())
     {
       res = av.getAlignment().getHiddenColumns()
-              .adjustForHiddenColumns(res);
+              .visibleToAbsoluteColumn(res);
     }
 
     if (!stretchingGroup)
@@ -275,7 +276,7 @@ public class ScalePanel extends Panel
     int res = (evt.getX() / av.getCharWidth())
             + av.getRanges().getStartRes();
     res = Math.max(0, res);
-    res = av.getAlignment().getHiddenColumns().adjustForHiddenColumns(res);
+    res = av.getAlignment().getHiddenColumns().visibleToAbsoluteColumn(res);
     res = Math.min(res, av.getAlignment().getWidth() - 1);
     min = Math.min(res, min);
     max = Math.max(res, max);
@@ -377,7 +378,7 @@ public class ScalePanel extends Panel
         {
           if (hidden.isVisible(sel))
           {
-            sel = hidden.findColumnPosition(sel);
+            sel = hidden.absoluteToVisibleColumn(sel);
           }
           else
           {
@@ -436,24 +437,17 @@ public class ScalePanel extends Panel
       if (av.getShowHiddenMarkers())
       {
         int widthx = 1 + endx - startx;
-        List<Integer> positions = hidden.findHiddenRegionPositions();
-        for (int pos : positions)
+        Iterator<Integer> it = hidden.getStartRegionIterator(startx,
+                startx + widthx + 1);
+        while (it.hasNext())
         {
-
-          res = pos - startx;
-
-          if (res < 0 || res > widthx)
-          {
-            continue;
-          }
+          res = it.next() - startx;
 
           gg.fillPolygon(
                   new int[]
-                  { -1 + res * avCharWidth - avcharHeight / 4,
-                      -1 + res * avCharWidth + avcharHeight / 4,
-                      -1 + res * avCharWidth },
-                  new int[]
-                  { y, y, y + 2 * yOf }, 3);
+                  { -1 + res * avCharWidth - avcharHeight / 4, -1 + res * avCharWidth + avcharHeight / 4,
+              -1 + res * avCharWidth }, new int[]
+          { y, y, y + 2 * yOf }, 3);
         }
       }
     }
diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 2420cf7..35d73de 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -25,6 +25,7 @@ import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.VisibleContigsIterator;
 import jalview.renderer.ScaleRenderer;
 import jalview.renderer.ScaleRenderer.ScaleMark;
 import jalview.viewmodel.AlignmentViewport;
@@ -37,7 +38,7 @@ import java.awt.Graphics;
 import java.awt.Image;
 import java.awt.Panel;
 import java.beans.PropertyChangeEvent;
-import java.util.List;
+import java.util.Iterator;
 
 public class SeqCanvas extends Panel implements ViewportListenerI
 {
@@ -130,16 +131,16 @@ public class SeqCanvas extends Panel implements ViewportListenerI
     if (av.hasHiddenColumns())
     {
       startx = av.getAlignment().getHiddenColumns()
-              .adjustForHiddenColumns(startx);
+              .visibleToAbsoluteColumn(startx);
       endx = av.getAlignment().getHiddenColumns()
-              .adjustForHiddenColumns(endx);
+              .visibleToAbsoluteColumn(endx);
     }
 
     int maxwidth = av.getAlignment().getWidth();
     if (av.hasHiddenColumns())
     {
       maxwidth = av.getAlignment().getHiddenColumns()
-              .findColumnPosition(maxwidth) - 1;
+              .absoluteToVisibleColumn(maxwidth) - 1;
     }
 
     // WEST SCALE
@@ -180,7 +181,7 @@ public class SeqCanvas extends Panel implements ViewportListenerI
     if (av.hasHiddenColumns())
     {
       endx = av.getAlignment().getHiddenColumns()
-              .adjustForHiddenColumns(endx);
+              .visibleToAbsoluteColumn(endx);
     }
 
     SequenceI seq;
@@ -417,71 +418,71 @@ public class SeqCanvas extends Panel implements ViewportListenerI
           int canvasHeight, int startRes)
   {
     AlignmentI al = av.getAlignment();
-
+  
     FontMetrics fm = getFontMetrics(av.getFont());
-
+  
     LABEL_EAST = 0;
     LABEL_WEST = 0;
-
+  
     if (av.getScaleRightWrapped())
     {
       LABEL_EAST = fm.stringWidth(getMask());
     }
-
+  
     if (av.getScaleLeftWrapped())
     {
       LABEL_WEST = fm.stringWidth(getMask());
     }
-
+  
     int hgap = avcharHeight;
     if (av.getScaleAboveWrapped())
     {
       hgap += avcharHeight;
     }
-
+  
     int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / avcharWidth;
     int cHeight = av.getAlignment().getHeight() * avcharHeight;
-
+  
     av.setWrappedWidth(cWidth);
-
+  
     av.getRanges().setViewportStartAndWidth(startRes, cWidth);
-
+  
     int endx;
     int ypos = hgap;
-
+  
     int maxwidth = av.getAlignment().getWidth();
-
+  
     if (av.hasHiddenColumns())
     {
       maxwidth = av.getAlignment().getHiddenColumns()
-              .findColumnPosition(maxwidth);
+              .absoluteToVisibleColumn(maxwidth);
     }
-
+  
     while ((ypos <= canvasHeight) && (startRes < maxwidth))
     {
       endx = startRes + cWidth - 1;
-
+  
       if (endx > maxwidth)
       {
         endx = maxwidth;
       }
-
+  
       g.setColor(Color.black);
-
+  
       if (av.getScaleLeftWrapped())
       {
         drawWestScale(g, startRes, endx, ypos);
       }
-
+  
       if (av.getScaleRightWrapped())
       {
         g.translate(canvasWidth - LABEL_EAST, 0);
         drawEastScale(g, startRes, endx, ypos);
         g.translate(-(canvasWidth - LABEL_EAST), 0);
       }
-
+  
       g.translate(LABEL_WEST, 0);
-
+  
       if (av.getScaleAboveWrapped())
       {
         drawNorthScale(g, startRes, endx, ypos);
@@ -491,37 +492,27 @@ public class SeqCanvas extends Panel implements ViewportListenerI
         HiddenColumns hidden = av.getAlignment().getHiddenColumns();
         g.setColor(Color.blue);
         int res;
-        List<Integer> positions = hidden.findHiddenRegionPositions();
-        for (int pos : positions)
+        Iterator<Integer> it = hidden.getStartRegionIterator(startRes,
+                endx + 1);
+        while (it.hasNext())
         {
-          res = pos - startRes;
-
-          if (res < 0 || res > endx - startRes)
-          {
-            continue;
-          }
-
+          res = it.next() - startRes;
           gg.fillPolygon(
                   new int[]
-                  { res * avcharWidth - avcharHeight / 4,
-                      res * avcharWidth + avcharHeight / 4,
-                      res * avcharWidth },
+                  { res * avcharWidth - avcharHeight / 4, res * avcharWidth + avcharHeight / 4, res * avcharWidth },
                   new int[]
-                  { ypos - (avcharHeight / 2), ypos - (avcharHeight / 2),
-                      ypos - (avcharHeight / 2) + 8 },
-                  3);
-
+                  { ypos - (avcharHeight / 2), ypos - (avcharHeight / 2), ypos - (avcharHeight / 2) + 8 }, 3);
         }
       }
-
+  
       if (g.getClip() == null)
       {
         g.setClip(0, 0, cWidth * avcharWidth, canvasHeight);
       }
-
+  
       drawPanel(g, startRes, endx, 0, al.getHeight() - 1, ypos);
       g.setClip(null);
-
+  
       if (av.isShowAnnotation())
       {
         g.translate(0, cHeight + ypos + 4);
@@ -529,17 +520,17 @@ public class SeqCanvas extends Panel implements ViewportListenerI
         {
           annotations = new AnnotationPanel(av);
         }
-
+  
         annotations.drawComponent(g, startRes, endx + 1);
         g.translate(0, -cHeight - ypos - 4);
       }
       g.translate(-LABEL_WEST, 0);
-
+  
       ypos += cHeight + getAnnotationHeight() + hgap;
-
+  
       startRes += cWidth;
     }
-
+  
   }
 
   AnnotationPanel annotations;
@@ -570,70 +561,44 @@ public class SeqCanvas extends Panel implements ViewportListenerI
     else
     {
       int screenY = 0;
-      final int screenYMax = endRes - startRes;
-      int blockStart = startRes;
-      int blockEnd = endRes;
-
-      if (av.hasHiddenColumns())
-      {
-        HiddenColumns hidden = av.getAlignment().getHiddenColumns();
-        for (int[] region : hidden.getHiddenColumnsCopy())
-        {
-          int hideStart = region[0];
-          int hideEnd = region[1];
-
-          if (hideStart <= blockStart)
-          {
-            blockStart += (hideEnd - hideStart) + 1;
-            continue;
-          }
-
-          /*
-           * draw up to just before the next hidden region, or the end of
-           * the visible region, whichever comes first
-           */
-          blockEnd = Math.min(hideStart - 1, blockStart + screenYMax
-                  - screenY);
-
-          g1.translate(screenY * avcharWidth, 0);
+      int blockStart;
+      int blockEnd;
 
-          draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
+      HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+      VisibleContigsIterator regions = (VisibleContigsIterator) hidden
+              .getVisContigsIterator(startRes, endRes + 1, true);
 
-          /*
-           * draw the downline of the hidden column marker (ScalePanel draws the
-           * triangle on top) if we reached it
-           */
-          if (av.getShowHiddenMarkers() && blockEnd == hideStart - 1)
-          {
-            g1.setColor(Color.blue);
-            g1.drawLine((blockEnd - blockStart + 1) * avcharWidth - 1,
-                    0 + offset,
-                    (blockEnd - blockStart + 1) * avcharWidth - 1,
-                    (endSeq - startSeq + 1) * avcharHeight + offset);
-          }
-
-          g1.translate(-screenY * avcharWidth, 0);
-          screenY += blockEnd - blockStart + 1;
-          blockStart = hideEnd + 1;
-
-          if (screenY > screenYMax)
-          {
-            // already rendered last block
-            return;
-          }
-        }
-      }
-      if (screenY <= screenYMax)
+      while (regions.hasNext())
       {
-        // remaining visible region to render
-        blockEnd = blockStart + (endRes - startRes) - screenY;
+        int[] region = regions.next();
+        blockEnd = region[1];
+        blockStart = region[0];
+
+        /*
+         * draw up to just before the next hidden region, or the end of
+         * the visible region, whichever comes first
+         */
         g1.translate(screenY * avcharWidth, 0);
+
         draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
 
+        /*
+         * draw the downline of the hidden column marker (ScalePanel draws the
+         * triangle on top) if we reached it
+         */
+        if (av.getShowHiddenMarkers()
+                && (regions.hasNext() || regions.endsAtHidden()))
+        {
+          g1.setColor(Color.blue);
+          g1.drawLine((blockEnd - blockStart + 1) * avcharWidth - 1,
+                  0 + offset, (blockEnd - blockStart + 1) * avcharWidth - 1,
+                  (endSeq - startSeq + 1) * avcharHeight + offset);
+        }
+
         g1.translate(-screenY * avcharWidth, 0);
+        screenY += blockEnd - blockStart + 1;
       }
     }
-
   }
 
   // int startRes, int endRes, int startSeq, int endSeq, int x, int y,
diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index d74bbb7..285c737 100644
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -647,7 +647,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     if (av.hasHiddenColumns())
     {
       res = av.getAlignment().getHiddenColumns()
-              .adjustForHiddenColumns(res);
+              .visibleToAbsoluteColumn(res);
     }
 
     return res;
@@ -1123,9 +1123,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     {
       fixedColumns = true;
       int y1 = av.getAlignment().getHiddenColumns()
-              .getHiddenBoundaryLeft(startres);
+              .getNextHiddenBoundary(true, startres);
       int y2 = av.getAlignment().getHiddenColumns()
-              .getHiddenBoundaryRight(startres);
+              .getNextHiddenBoundary(false, startres);
 
       if ((insertGap && startres > y1 && lastres < y1)
               || (!insertGap && startres < y2 && lastres > y2))
@@ -1197,7 +1197,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
           if (sg.getSize() == av.getAlignment().getHeight())
           {
             if ((av.hasHiddenColumns() && startres < av.getAlignment()
-                    .getHiddenColumns().getHiddenBoundaryRight(startres)))
+                    .getHiddenColumns()
+                    .getNextHiddenBoundary(false, startres)))
             {
               endEditing();
               return;
@@ -1497,7 +1498,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
     // always do this - annotation has own state
     // but defer colourscheme update until hidden sequences are passed in
-    boolean vischange = stretchGroup.recalcConservation(true);
+    boolean vischange = stretchGroup.recalcAnnotations(true);
     // here we rely on stretchGroup == av.getSelection()
     needOverviewUpdate |= vischange && av.isSelectionDefinedGroup()
             && afterDrag;
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index dc50843..dcd6546 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -281,7 +281,7 @@ public class Cache
     @Override
     public synchronized Enumeration<Object> keys()
     {
-      return Collections.enumeration(new TreeSet<Object>(super.keySet()));
+      return Collections.enumeration(new TreeSet<>(super.keySet()));
     }
   };
 
@@ -334,7 +334,10 @@ public class Cache
     }
   }
 
-  /** Called when Jalview is started */
+  /**
+   * Loads properties from the given properties file. Any existing properties
+   * are first cleared.
+   */
   public static void loadProperties(String propsFile)
   {
     propertiesFile = propsFile;
@@ -369,6 +372,7 @@ public class Cache
       {
         fis = new FileInputStream(propertiesFile);
       }
+      applicationProperties.clear();
       applicationProperties.load(fis);
 
       // remove any old build properties
@@ -621,14 +625,14 @@ public class Cache
    * @param obj
    *          String value of property
    * 
-   * @return String value of property
+   * @return previous value of property (or null)
    */
-  public static String setProperty(String key, String obj)
+  public static Object setProperty(String key, String obj)
   {
-
+    Object oldValue = null;
     try
     {
-      applicationProperties.setProperty(key, obj);
+      oldValue = applicationProperties.setProperty(key, obj);
       if (!propsAreReadOnly)
       {
         FileOutputStream out = new FileOutputStream(propertiesFile);
@@ -640,7 +644,7 @@ public class Cache
       System.out.println(
               "Error setting property: " + key + " " + obj + "\n" + ex);
     }
-    return obj;
+    return oldValue;
   }
 
   /**
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 9ec0033..bc93c37 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -20,9 +20,6 @@
  */
 package jalview.bin;
 
-import groovy.lang.Binding;
-import groovy.util.GroovyScriptEngine;
-
 import jalview.ext.so.SequenceOntology;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
@@ -66,6 +63,9 @@ import java.util.Vector;
 
 import javax.swing.UIManager;
 
+import groovy.lang.Binding;
+import groovy.util.GroovyScriptEngine;
+
 /**
  * Main class for Jalview Application <br>
  * <br>
@@ -175,6 +175,8 @@ public class Jalview
    * 
    * @param args
    *          open <em>filename</em>
+   * @throws InterruptedException
+   * @throws IOException
    */
   public static void main(String[] args)
   {
@@ -184,6 +186,8 @@ public class Jalview
 
   /**
    * @param args
+   * @throws InterruptedException
+   * @throws IOException
    */
   void doMain(String[] args)
   {
@@ -970,7 +974,7 @@ public class Jalview
     }
     try
     {
-      Map<String, Object> vbinding = new HashMap<String, Object>();
+      Map<String, Object> vbinding = new HashMap<>();
       vbinding.put("Jalview", this);
       if (af != null)
       {
@@ -1036,7 +1040,7 @@ public class Jalview
                         + nickname + "|" + url);
         if (source == null)
         {
-          source = new Vector<String>();
+          source = new Vector<>();
         }
         source.addElement(nickname);
       }
@@ -1054,7 +1058,7 @@ public class Jalview
       System.out.println("adding source '" + data + "'");
       if (source == null)
       {
-        source = new Vector<String>();
+        source = new Vector<>();
       }
       source.addElement(data);
     }
diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 6504290..a60496c 100644
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -31,7 +31,6 @@ import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentOrder;
 import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
@@ -471,7 +470,7 @@ public class JalviewLite extends Applet
         SequenceI rs = sel.getSequenceAt(0);
         start = rs.findIndex(start);
         end = rs.findIndex(end);
-        List<Integer> cs = new ArrayList<Integer>(csel.getSelected());
+        List<Integer> cs = new ArrayList<>(csel.getSelected());
         csel.clear();
         for (Integer selectedCol : cs)
         {
@@ -921,7 +920,7 @@ public class JalviewLite extends Applet
     setMouseoverListener(currentAlignFrame, listener);
   }
 
-  private Vector<jalview.javascript.JSFunctionExec> javascriptListeners = new Vector<jalview.javascript.JSFunctionExec>();
+  private Vector<jalview.javascript.JSFunctionExec> javascriptListeners = new Vector<>();
 
   /*
    * (non-Javadoc)
@@ -2165,8 +2164,8 @@ public class JalviewLite extends Applet
           else
           {
             param = st.nextToken();
-            List<SequenceI> tmp = new ArrayList<SequenceI>();
-            List<String> tmp2 = new ArrayList<String>();
+            List<SequenceI> tmp = new ArrayList<>();
+            List<String> tmp2 = new ArrayList<>();
 
             while (st.hasMoreTokens())
             {
@@ -2279,12 +2278,9 @@ public class JalviewLite extends Applet
           JnetAnnotationMaker.add_annotation(predictions,
                   alignFrame.viewport.getAlignment(), 0, false);
           // false == do not add sequence profile from concise output
-          SequenceI repseq = alignFrame.viewport.getAlignment()
-                  .getSequenceAt(0);
-          alignFrame.viewport.getAlignment().setSeqrep(repseq);
-          HiddenColumns cs = new HiddenColumns();
-          cs.hideInsertionsFor(repseq);
-          alignFrame.viewport.getAlignment().setHiddenColumns(cs);
+
+          alignFrame.viewport.getAlignment().setupJPredAlignment();
+
           alignFrame.alignPanel.fontChanged();
           alignFrame.alignPanel.setScrollValues(0, 0);
           result = true;
@@ -2802,9 +2798,9 @@ public class JalviewLite extends Applet
     // callInitCallback();
   }
 
-  private Hashtable<String, long[]> jshashes = new Hashtable<String, long[]>();
+  private Hashtable<String, long[]> jshashes = new Hashtable<>();
 
-  private Hashtable<String, Hashtable<String, String[]>> jsmessages = new Hashtable<String, Hashtable<String, String[]>>();
+  private Hashtable<String, Hashtable<String, String[]>> jsmessages = new Hashtable<>();
 
   public void setJsMessageSet(String messageclass, String viewId,
           String[] colcommands)
@@ -2812,7 +2808,7 @@ public class JalviewLite extends Applet
     Hashtable<String, String[]> msgset = jsmessages.get(messageclass);
     if (msgset == null)
     {
-      msgset = new Hashtable<String, String[]>();
+      msgset = new Hashtable<>();
       jsmessages.put(messageclass, msgset);
     }
     msgset.put(viewId, colcommands);
diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index f268d37..6b100ea 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -29,10 +29,12 @@ import jalview.util.MessageManager;
 
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.BitSet;
 import java.util.Collections;
 import java.util.Enumeration;
 import java.util.HashSet;
 import java.util.Hashtable;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
@@ -49,7 +51,9 @@ public class Alignment implements AlignmentI
 {
   private Alignment dataset;
 
-  protected List<SequenceI> sequences;
+  private List<SequenceI> sequences;
+
+  private SequenceI hmmConsensus;
 
   protected List<SequenceGroup> groups;
 
@@ -198,6 +202,7 @@ public class Alignment implements AlignmentI
         return sequences.get(i);
       }
     }
+
     return null;
   }
 
@@ -288,6 +293,32 @@ public class Alignment implements AlignmentI
   }
 
   /**
+   * Inserts a sequence at a point in the alignment.
+   * 
+   * @param i
+   *          the index of the position the sequence is to be inserted in.
+   */
+  @Override
+  public void insertSequenceAt(int i, SequenceI snew)
+  {
+    synchronized (sequences)
+    {
+      if (sequences.size() > i)
+      {
+        sequences.add(i, snew);
+        return;
+
+      }
+      else
+      {
+        sequences.add(snew);
+        hiddenSequences.adjustHeightSequenceAdded();
+      }
+      return;
+    }
+  }
+
+  /**
    * DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
@@ -706,7 +737,7 @@ public class Alignment implements AlignmentI
   public int getWidth()
   {
     int maxLength = -1;
-
+  
     for (int i = 0; i < sequences.size(); i++)
     {
       if (getSequenceAt(i).getLength() > maxLength)
@@ -714,9 +745,34 @@ public class Alignment implements AlignmentI
         maxLength = getSequenceAt(i).getLength();
       }
     }
-
+  
     return maxLength;
   }
+  /*
+  @Override
+  public int getWidth()
+  {
+    final Wrapper temp = new Wrapper();
+  
+    forEachSequence(new Consumer<SequenceI>()
+    {
+      @Override
+      public void accept(SequenceI s)
+      {
+        if (s.getLength() > temp.inner)
+        {
+          temp.inner = s.getLength();
+        }
+      }
+    }, 0, sequences.size() - 1);
+  
+    return temp.inner;
+  }
+  
+  public static class Wrapper
+  {
+    public int inner;
+  }*/
 
   /**
    * DOCUMENT ME!
@@ -1603,7 +1659,10 @@ public class Alignment implements AlignmentI
     AlignmentAnnotation annot = new AlignmentAnnotation(name, name,
             new Annotation[1], 0f, 0f, AlignmentAnnotation.BAR_GRAPH);
     annot.hasText = false;
-    annot.setCalcId(new String(calcId));
+    if (calcId != null)
+    {
+      annot.setCalcId(calcId);
+    }
     annot.autoCalculated = autoCalc;
     if (seqRef != null)
     {
@@ -1895,4 +1954,128 @@ public class Alignment implements AlignmentI
   {
     hiddenCols = cols;
   }
+
+  @Override
+  public SequenceI getHmmConsensus()
+  {
+    return hmmConsensus;
+  }
+
+  @Override
+  public void setHmmConsensus(SequenceI hmmConsensus)
+  {
+    this.hmmConsensus = hmmConsensus;
+  }
+
+  @Override
+  public void setupJPredAlignment()
+  {
+    SequenceI repseq = getSequenceAt(0);
+    setSeqrep(repseq);
+    HiddenColumns cs = new HiddenColumns();
+    cs.hideList(repseq.getInsertions());
+    setHiddenColumns(cs);
+  }
+
+  @Override
+  public HiddenColumns propagateInsertions(SequenceI profileseq,
+          AlignmentView input)
+  {
+    int profsqpos = 0;
+
+    char gc = getGapCharacter();
+    Object[] alandhidden = input.getAlignmentAndHiddenColumns(gc);
+    HiddenColumns nview = (HiddenColumns) alandhidden[1];
+    SequenceI origseq = ((SequenceI[]) alandhidden[0])[profsqpos];
+    return propagateInsertions(profileseq, origseq, nview);
+  }
+
+  /**
+   * 
+   * @param profileseq
+   *          sequence in al which corresponds to origseq
+   * @param al
+   *          alignment which is to have gaps inserted into it
+   * @param origseq
+   *          sequence corresponding to profileseq which defines gap map for
+   *          modifying al
+   */
+  private HiddenColumns propagateInsertions(SequenceI profileseq,
+          SequenceI origseq, HiddenColumns hc)
+  {
+    // take the set of hidden columns, and the set of gaps in origseq,
+    // and remove all the hidden gaps from hiddenColumns
+
+    // first get the gaps as a Bitset
+    // then calculate hidden ^ not(gap)
+    BitSet gaps = origseq.gapBitset();
+    hc.andNot(gaps);
+
+    // for each sequence in the alignment, except the profile sequence,
+    // insert gaps corresponding to each hidden region but where each hidden
+    // column region is shifted backwards by the number of preceding visible
+    // gaps update hidden columns at the same time
+    HiddenColumns newhidden = new HiddenColumns();
+
+    int numGapsBefore = 0;
+    int gapPosition = 0;
+    Iterator<int[]> it = hc.iterator();
+    while (it.hasNext())
+    {
+      int[] region = it.next();
+
+      // get region coordinates accounting for gaps
+      // we can rely on gaps not being *in* hidden regions because we already
+      // removed those
+      while (gapPosition < region[0])
+      {
+        gapPosition++;
+        if (gaps.get(gapPosition))
+        {
+          numGapsBefore++;
+        }
+      }
+
+      int left = region[0] - numGapsBefore;
+      int right = region[1] - numGapsBefore;
+
+      newhidden.hideColumns(left, right);
+      padGaps(left, right, profileseq);
+    }
+    return newhidden;
+  }
+
+  /**
+   * Pad gaps in all sequences in alignment except profileseq
+   * 
+   * @param left
+   *          position of first gap to insert
+   * @param right
+   *          position of last gap to insert
+   * @param profileseq
+   *          sequence not to pad
+   */
+  private void padGaps(int left, int right, SequenceI profileseq)
+  {
+    char gc = getGapCharacter();
+
+    // make a string with number of gaps = length of hidden region
+    StringBuilder sb = new StringBuilder();
+    for (int g = 0; g < right - left + 1; g++)
+    {
+      sb.append(gc);
+    }
+
+    // loop over the sequences and pad with gaps where required
+    for (int s = 0, ns = getHeight(); s < ns; s++)
+    {
+      SequenceI sqobj = getSequenceAt(s);
+      if ((sqobj != profileseq) && (sqobj.getLength() >= left))
+      {
+        String sq = sqobj.getSequenceAsString();
+        sqobj.setSequence(
+                sq.substring(0, left) + sb.toString() + sq.substring(left));
+      }
+    }
+  }
 }
diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index f7bf4d8..0f7883e 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -94,76 +94,6 @@ public class AlignmentAnnotation
   private long invalidrnastruc = -2;
 
   /**
-   * Updates the _rnasecstr field Determines the positions that base pair and
-   * the positions of helices based on secondary structure from a Stockholm file
-   * 
-   * @param rnaAnnotation
-   */
-  private void _updateRnaSecStr(CharSequence rnaAnnotation)
-  {
-    try
-    {
-      _rnasecstr = Rna.getHelixMap(rnaAnnotation);
-      invalidrnastruc = -1;
-    } catch (WUSSParseException px)
-    {
-      // DEBUG System.out.println(px);
-      invalidrnastruc = px.getProblemPos();
-    }
-    if (invalidrnastruc > -1)
-    {
-      return;
-    }
-
-    if (_rnasecstr != null && _rnasecstr.length > 0)
-    {
-      // show all the RNA secondary structure annotation symbols.
-      isrna = true;
-      showAllColLabels = true;
-      scaleColLabel = true;
-      _markRnaHelices();
-    }
-    // System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup());
-
-  }
-
-  private void _markRnaHelices()
-  {
-    int mxval = 0;
-    // Figure out number of helices
-    // Length of rnasecstr is the number of pairs of positions that base pair
-    // with each other in the secondary structure
-    for (int x = 0; x < _rnasecstr.length; x++)
-    {
-
-      /*
-       * System.out.println(this.annotation._rnasecstr[x] + " Begin" +
-       * this.annotation._rnasecstr[x].getBegin());
-       */
-      // System.out.println(this.annotation._rnasecstr[x].getFeatureGroup());
-      int val = 0;
-      try
-      {
-        val = Integer.valueOf(_rnasecstr[x].getFeatureGroup());
-        if (mxval < val)
-        {
-          mxval = val;
-        }
-      } catch (NumberFormatException q)
-      {
-      }
-      ;
-
-      annotations[_rnasecstr[x].getBegin()].value = val;
-      annotations[_rnasecstr[x].getEnd()].value = val;
-
-      // annotations[_rnasecstr[x].getBegin()].displayCharacter = "" + val;
-      // annotations[_rnasecstr[x].getEnd()].displayCharacter = "" + val;
-    }
-    setScore(mxval);
-  }
-
-  /**
    * map of positions in the associated annotation
    */
   private Map<Integer, Annotation> sequenceMapping;
@@ -258,27 +188,266 @@ public class AlignmentAnnotation
     }
   }
 
-  /**
-   * Creates a new AlignmentAnnotation object.
-   * 
-   * @param label
-   *          short label shown under sequence labels
-   * @param description
-   *          text displayed on mouseover
-   * @param annotations
-   *          set of positional annotation elements
-   */
-  public AlignmentAnnotation(String label, String description,
-          Annotation[] annotations)
-  {
-    setAnnotationId();
-    // always editable?
-    editable = true;
-    this.label = label;
-    this.description = description;
-    this.annotations = annotations;
+  /**
+   * Creates a new AlignmentAnnotation object.
+   * 
+   * @param label
+   *          short label shown under sequence labels
+   * @param description
+   *          text displayed on mouseover
+   * @param annotations
+   *          set of positional annotation elements
+   */
+  public AlignmentAnnotation(String label, String description,
+          Annotation[] annotations)
+  {
+    setAnnotationId();
+    // always editable?
+    editable = true;
+    this.label = label;
+    this.description = description;
+    this.annotations = annotations;
+
+    validateRangeAndDisplay();
+  }
+
+  /**
+   * Copy constructor creates a new independent annotation row with the same
+   * associated sequenceRef
+   * 
+   * @param annotation
+   */
+  public AlignmentAnnotation(AlignmentAnnotation annotation)
+  {
+    setAnnotationId();
+    this.label = new String(annotation.label);
+    if (annotation.description != null)
+    {
+      this.description = new String(annotation.description);
+    }
+    this.graphMin = annotation.graphMin;
+    this.graphMax = annotation.graphMax;
+    this.graph = annotation.graph;
+    this.graphHeight = annotation.graphHeight;
+    this.graphGroup = annotation.graphGroup;
+    this.groupRef = annotation.groupRef;
+    this.editable = annotation.editable;
+    this.autoCalculated = annotation.autoCalculated;
+    this.hasIcons = annotation.hasIcons;
+    this.hasText = annotation.hasText;
+    this.height = annotation.height;
+    this.label = annotation.label;
+    this.padGaps = annotation.padGaps;
+    this.visible = annotation.visible;
+    this.centreColLabels = annotation.centreColLabels;
+    this.scaleColLabel = annotation.scaleColLabel;
+    this.showAllColLabels = annotation.showAllColLabels;
+    this.calcId = annotation.calcId;
+    if (annotation.properties != null)
+    {
+      properties = new HashMap<>();
+      for (Map.Entry<String, String> val : annotation.properties.entrySet())
+      {
+        properties.put(val.getKey(), val.getValue());
+      }
+    }
+    if (this.hasScore = annotation.hasScore)
+    {
+      this.score = annotation.score;
+    }
+    if (annotation.threshold != null)
+    {
+      threshold = new GraphLine(annotation.threshold);
+    }
+    Annotation[] ann = annotation.annotations;
+    if (annotation.annotations != null)
+    {
+      this.annotations = new Annotation[ann.length];
+      for (int i = 0; i < ann.length; i++)
+      {
+        if (ann[i] != null)
+        {
+          annotations[i] = new Annotation(ann[i]);
+          if (_linecolour != null)
+          {
+            _linecolour = annotations[i].colour;
+          }
+        }
+      }
+    }
+    if (annotation.sequenceRef != null)
+    {
+      this.sequenceRef = annotation.sequenceRef;
+      if (annotation.sequenceMapping != null)
+      {
+        Integer p = null;
+        sequenceMapping = new HashMap<>();
+        Iterator<Integer> pos = annotation.sequenceMapping.keySet()
+                .iterator();
+        while (pos.hasNext())
+        {
+          // could optimise this!
+          p = pos.next();
+          Annotation a = annotation.sequenceMapping.get(p);
+          if (a == null)
+          {
+            continue;
+          }
+          if (ann != null)
+          {
+            for (int i = 0; i < ann.length; i++)
+            {
+              if (ann[i] == a)
+              {
+                sequenceMapping.put(p, annotations[i]);
+              }
+            }
+          }
+        }
+      }
+      else
+      {
+        this.sequenceMapping = null;
+      }
+    }
+    // TODO: check if we need to do this: JAL-952
+    // if (this.isrna=annotation.isrna)
+    {
+      // _rnasecstr=new SequenceFeature[annotation._rnasecstr];
+    }
+    validateRangeAndDisplay(); // construct hashcodes, etc.
+  }
+
+  /**
+   * copy constructor with edit based on the hidden columns marked in colSel
+   * 
+   * @param alignmentAnnotation
+   * @param colSel
+   */
+  public AlignmentAnnotation(AlignmentAnnotation alignmentAnnotation,
+          HiddenColumns hidden)
+  {
+    this(alignmentAnnotation);
+    if (annotations == null)
+    {
+      return;
+    }
+    makeVisibleAnnotation(hidden);
+  }
+
+  /**
+   * Creates a new AlignmentAnnotation object.
+   * 
+   * @param label
+   *          DOCUMENT ME!
+   * @param description
+   *          DOCUMENT ME!
+   * @param annotations
+   *          DOCUMENT ME!
+   * @param min
+   *          DOCUMENT ME!
+   * @param max
+   *          DOCUMENT ME!
+   * @param winLength
+   *          DOCUMENT ME!
+   */
+  public AlignmentAnnotation(String label, String description,
+          Annotation[] annotations, float min, float max, int graphType)
+  {
+    setAnnotationId();
+    // graphs are not editable
+    editable = graphType == 0;
+
+    this.label = label;
+    this.description = description;
+    this.annotations = annotations;
+    graph = graphType;
+    graphMin = min;
+    graphMax = max;
+    validateRangeAndDisplay();
+  }
+
+  /**
+   * Score only annotation
+   * 
+   * @param label
+   * @param description
+   * @param score
+   */
+  public AlignmentAnnotation(String label, String description, double score)
+  {
+    this(label, description, null);
+    setScore(score);
+  }
+
+  /**
+   * Updates the _rnasecstr field Determines the positions that base pair and
+   * the positions of helices based on secondary structure from a Stockholm file
+   * 
+   * @param rnaAnnotation
+   */
+  private void _updateRnaSecStr(CharSequence rnaAnnotation)
+  {
+    try
+    {
+      _rnasecstr = Rna.getHelixMap(rnaAnnotation);
+      invalidrnastruc = -1;
+    } catch (WUSSParseException px)
+    {
+      // DEBUG System.out.println(px);
+      invalidrnastruc = px.getProblemPos();
+    }
+    if (invalidrnastruc > -1)
+    {
+      return;
+    }
+
+    if (_rnasecstr != null && _rnasecstr.length > 0)
+    {
+      // show all the RNA secondary structure annotation symbols.
+      isrna = true;
+      showAllColLabels = true;
+      scaleColLabel = true;
+      _markRnaHelices();
+    }
+    // System.out.println("featuregroup " + _rnasecstr[0].getFeatureGroup());
+
+  }
+
+  private void _markRnaHelices()
+  {
+    int mxval = 0;
+    // Figure out number of helices
+    // Length of rnasecstr is the number of pairs of positions that base pair
+    // with each other in the secondary structure
+    for (int x = 0; x < _rnasecstr.length; x++)
+    {
+
+      /*
+       * System.out.println(this.annotation._rnasecstr[x] + " Begin" +
+       * this.annotation._rnasecstr[x].getBegin());
+       */
+      // System.out.println(this.annotation._rnasecstr[x].getFeatureGroup());
+      int val = 0;
+      try
+      {
+        val = Integer.valueOf(_rnasecstr[x].getFeatureGroup());
+        if (mxval < val)
+        {
+          mxval = val;
+        }
+      } catch (NumberFormatException q)
+      {
+      }
+      ;
+
+      annotations[_rnasecstr[x].getBegin()].value = val;
+      annotations[_rnasecstr[x].getEnd()].value = val;
 
-    validateRangeAndDisplay();
+      // annotations[_rnasecstr[x].getBegin()].displayCharacter = "" + val;
+      // annotations[_rnasecstr[x].getEnd()].displayCharacter = "" + val;
+    }
+    setScore(mxval);
   }
 
   /**
@@ -521,38 +690,6 @@ public class AlignmentAnnotation
   }
 
   /**
-   * Creates a new AlignmentAnnotation object.
-   * 
-   * @param label
-   *          DOCUMENT ME!
-   * @param description
-   *          DOCUMENT ME!
-   * @param annotations
-   *          DOCUMENT ME!
-   * @param min
-   *          DOCUMENT ME!
-   * @param max
-   *          DOCUMENT ME!
-   * @param winLength
-   *          DOCUMENT ME!
-   */
-  public AlignmentAnnotation(String label, String description,
-          Annotation[] annotations, float min, float max, int graphType)
-  {
-    setAnnotationId();
-    // graphs are not editable
-    editable = graphType == 0;
-
-    this.label = label;
-    this.description = description;
-    this.annotations = annotations;
-    graph = graphType;
-    graphMin = min;
-    graphMax = max;
-    validateRangeAndDisplay();
-  }
-
-  /**
    * checks graphMin and graphMax, secondary structure symbols, sets graphType
    * appropriately, sets null labels to the empty string if appropriate.
    */
@@ -633,113 +770,6 @@ public class AlignmentAnnotation
   }
 
   /**
-   * Copy constructor creates a new independent annotation row with the same
-   * associated sequenceRef
-   * 
-   * @param annotation
-   */
-  public AlignmentAnnotation(AlignmentAnnotation annotation)
-  {
-    setAnnotationId();
-    this.label = new String(annotation.label);
-    if (annotation.description != null)
-    {
-      this.description = new String(annotation.description);
-    }
-    this.graphMin = annotation.graphMin;
-    this.graphMax = annotation.graphMax;
-    this.graph = annotation.graph;
-    this.graphHeight = annotation.graphHeight;
-    this.graphGroup = annotation.graphGroup;
-    this.groupRef = annotation.groupRef;
-    this.editable = annotation.editable;
-    this.autoCalculated = annotation.autoCalculated;
-    this.hasIcons = annotation.hasIcons;
-    this.hasText = annotation.hasText;
-    this.height = annotation.height;
-    this.label = annotation.label;
-    this.padGaps = annotation.padGaps;
-    this.visible = annotation.visible;
-    this.centreColLabels = annotation.centreColLabels;
-    this.scaleColLabel = annotation.scaleColLabel;
-    this.showAllColLabels = annotation.showAllColLabels;
-    this.calcId = annotation.calcId;
-    if (annotation.properties != null)
-    {
-      properties = new HashMap<String, String>();
-      for (Map.Entry<String, String> val : annotation.properties.entrySet())
-      {
-        properties.put(val.getKey(), val.getValue());
-      }
-    }
-    if (this.hasScore = annotation.hasScore)
-    {
-      this.score = annotation.score;
-    }
-    if (annotation.threshold != null)
-    {
-      threshold = new GraphLine(annotation.threshold);
-    }
-    Annotation[] ann = annotation.annotations;
-    if (annotation.annotations != null)
-    {
-      this.annotations = new Annotation[ann.length];
-      for (int i = 0; i < ann.length; i++)
-      {
-        if (ann[i] != null)
-        {
-          annotations[i] = new Annotation(ann[i]);
-          if (_linecolour != null)
-          {
-            _linecolour = annotations[i].colour;
-          }
-        }
-      }
-    }
-    if (annotation.sequenceRef != null)
-    {
-      this.sequenceRef = annotation.sequenceRef;
-      if (annotation.sequenceMapping != null)
-      {
-        Integer p = null;
-        sequenceMapping = new HashMap<Integer, Annotation>();
-        Iterator<Integer> pos = annotation.sequenceMapping.keySet()
-                .iterator();
-        while (pos.hasNext())
-        {
-          // could optimise this!
-          p = pos.next();
-          Annotation a = annotation.sequenceMapping.get(p);
-          if (a == null)
-          {
-            continue;
-          }
-          if (ann != null)
-          {
-            for (int i = 0; i < ann.length; i++)
-            {
-              if (ann[i] == a)
-              {
-                sequenceMapping.put(p, annotations[i]);
-              }
-            }
-          }
-        }
-      }
-      else
-      {
-        this.sequenceMapping = null;
-      }
-    }
-    // TODO: check if we need to do this: JAL-952
-    // if (this.isrna=annotation.isrna)
-    {
-      // _rnasecstr=new SequenceFeature[annotation._rnasecstr];
-    }
-    validateRangeAndDisplay(); // construct hashcodes, etc.
-  }
-
-  /**
    * clip the annotation to the columns given by startRes and endRes (inclusive)
    * and prune any existing sequenceMapping to just those columns.
    * 
@@ -782,7 +812,7 @@ public class AlignmentAnnotation
       int epos = sequenceRef.findPosition(endRes);
       if (sequenceMapping != null)
       {
-        Map<Integer, Annotation> newmapping = new HashMap<Integer, Annotation>();
+        Map<Integer, Annotation> newmapping = new HashMap<>();
         Iterator<Integer> e = sequenceMapping.keySet().iterator();
         while (e.hasNext())
         {
@@ -909,7 +939,7 @@ public class AlignmentAnnotation
     {
       return;
     }
-    sequenceMapping = new HashMap<Integer, Annotation>();
+    sequenceMapping = new HashMap<>();
 
     int seqPos;
 
@@ -1097,36 +1127,6 @@ public class AlignmentAnnotation
     return hasScore || !Double.isNaN(score);
   }
 
-  /**
-   * Score only annotation
-   * 
-   * @param label
-   * @param description
-   * @param score
-   */
-  public AlignmentAnnotation(String label, String description, double score)
-  {
-    this(label, description, null);
-    setScore(score);
-  }
-
-  /**
-   * copy constructor with edit based on the hidden columns marked in colSel
-   * 
-   * @param alignmentAnnotation
-   * @param colSel
-   */
-  public AlignmentAnnotation(AlignmentAnnotation alignmentAnnotation,
-          HiddenColumns hidden)
-  {
-    this(alignmentAnnotation);
-    if (annotations == null)
-    {
-      return;
-    }
-    hidden.makeVisibleAnnotation(this);
-  }
-
   public void setPadGaps(boolean padgaps, char gapchar)
   {
     this.padGaps = padgaps;
@@ -1185,12 +1185,12 @@ public class AlignmentAnnotation
   /**
    * machine readable ID string indicating what generated this annotation
    */
-  protected String calcId = "";
+  private String calcId = "";
 
   /**
    * properties associated with the calcId
    */
-  protected Map<String, String> properties = new HashMap<String, String>();
+  protected Map<String, String> properties = new HashMap<>();
 
   /**
    * base colour for line graphs. If null, will be set automatically by
@@ -1236,7 +1236,7 @@ public class AlignmentAnnotation
             : false;
 
     // TODO build a better annotation element map and get rid of annotations[]
-    Map<Integer, Annotation> mapForsq = new HashMap<Integer, Annotation>();
+    Map<Integer, Annotation> mapForsq = new HashMap<>();
     if (sequenceMapping != null)
     {
       if (sp2sq != null)
@@ -1289,7 +1289,7 @@ public class AlignmentAnnotation
     if (mapping != null)
     {
       Map<Integer, Annotation> old = sequenceMapping;
-      Map<Integer, Annotation> remap = new HashMap<Integer, Annotation>();
+      Map<Integer, Annotation> remap = new HashMap<>();
       int index = -1;
       for (int mp[] : mapping.values())
       {
@@ -1347,7 +1347,7 @@ public class AlignmentAnnotation
   {
     if (properties == null)
     {
-      properties = new HashMap<String, String>();
+      properties = new HashMap<>();
     }
     properties.put(property, value);
   }
@@ -1473,12 +1473,120 @@ public class AlignmentAnnotation
     return graphMin < graphMax;
   }
 
+  /**
+   * delete any columns in alignmentAnnotation that are hidden (including
+   * sequence associated annotation).
+   * 
+   * @param hiddenColumns
+   *          the set of hidden columns
+   */
+  public void makeVisibleAnnotation(HiddenColumns hiddenColumns)
+  {
+    if (annotations != null)
+    {
+      makeVisibleAnnotation(0, annotations.length, hiddenColumns);
+    }
+  }
+
+  /**
+   * delete any columns in alignmentAnnotation that are hidden (including
+   * sequence associated annotation).
+   * 
+   * @param start
+   *          remove any annotation to the right of this column
+   * @param end
+   *          remove any annotation to the left of this column
+   * @param hiddenColumns
+   *          the set of hidden columns
+   */
+  public void makeVisibleAnnotation(int start, int end,
+          HiddenColumns hiddenColumns)
+  {
+    if (annotations != null)
+    {
+      if (hiddenColumns.hasHiddenColumns())
+      {
+        removeHiddenAnnotation(start, end, hiddenColumns);
+      }
+      else
+      {
+        restrict(start, end);
+      }
+    }
+  }
+
+  /**
+   * The actual implementation of deleting hidden annotation columns
+   * 
+   * @param start
+   *          remove any annotation to the right of this column
+   * @param end
+   *          remove any annotation to the left of this column
+   * @param hiddenColumns
+   *          the set of hidden columns
+   */
+  private void removeHiddenAnnotation(int start, int end,
+          HiddenColumns hiddenColumns)
+  {
+    // mangle the alignmentAnnotation annotation array
+    ArrayList<Annotation[]> annels = new ArrayList<>();
+    Annotation[] els = null;
+
+    int w = 0;
+
+    Iterator<int[]> blocks = hiddenColumns.getVisContigsIterator(start,
+            end + 1, false);
+
+    int copylength;
+    int annotationLength;
+    while (blocks.hasNext())
+    {
+      int[] block = blocks.next();
+      annotationLength = block[1] - block[0] + 1;
+
+      if (blocks.hasNext())
+      {
+        // copy just the visible segment of the annotation row
+        copylength = annotationLength;
+      }
+      else
+      {
+        if (annotationLength + block[0] <= annotations.length)
+        {
+          // copy just the visible segment of the annotation row
+          copylength = annotationLength;
+        }
+        else
+        {
+          // copy to the end of the annotation row
+          copylength = annotations.length - block[0];
+        }
+      }
+
+      els = new Annotation[annotationLength];
+      annels.add(els);
+      System.arraycopy(annotations, block[0], els, 0, copylength);
+      w += annotationLength;
+    }
+
+    if (w != 0)
+    {
+      annotations = new Annotation[w];
+
+      w = 0;
+      for (Annotation[] chnk : annels)
+      {
+        System.arraycopy(chnk, 0, annotations, w, chnk.length);
+        w += chnk.length;
+      }
+    }
+  }
+
   public static Iterable<AlignmentAnnotation> findAnnotations(
           Iterable<AlignmentAnnotation> list, SequenceI seq, String calcId,
           String label)
   {
-
-    ArrayList<AlignmentAnnotation> aa = new ArrayList<>();
+    List<AlignmentAnnotation> aa = new ArrayList<>();
     for (AlignmentAnnotation ann : list)
     {
       if ((calcId == null || (ann.getCalcId() != null
@@ -1522,7 +1630,6 @@ public class AlignmentAnnotation
   public static Iterable<AlignmentAnnotation> findAnnotation(
           List<AlignmentAnnotation> list, String calcId)
   {
-
     List<AlignmentAnnotation> aa = new ArrayList<>();
     if (calcId == null)
     {
diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 084b80e..d591f42 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -504,8 +504,6 @@ public interface AlignmentI extends AnnotatedCollectionI
    *          - null or specific sequence reference
    * @param groupRef
    *          - null or specific group reference
-   * @param method
-   *          - CalcId for the annotation (must match)
    * 
    * @return existing annotation matching the given attributes
    */
@@ -580,6 +578,41 @@ public interface AlignmentI extends AnnotatedCollectionI
    */
   AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo);
 
+  /**
+   * Set the hidden columns collection on the alignment
+   * 
+   * @param cols
+   */
   public void setHiddenColumns(HiddenColumns cols);
 
+  /**
+   * Insert a sequence at a position in an alignment
+   * 
+   * @param i
+   *          The index of the position.
+   * @param snew
+   *          The new sequence.
+   */
+  void insertSequenceAt(int i, SequenceI snew);
+
+  /**
+   * Set the first sequence as representative and hide its insertions. Typically
+   * used when loading JPred files.
+   */
+  public void setupJPredAlignment();
+
+  /**
+   * Add gaps into the sequences aligned to profileseq under the given
+   * AlignmentView
+   * 
+   * @param profileseq
+   *          sequence in al which sequences are aligned to
+   * @param input
+   *          alignment view where sequence corresponding to profileseq is first
+   *          entry
+   * @return new HiddenColumns for new alignment view, with insertions into
+   *         profileseq marked as hidden.
+   */
+  public HiddenColumns propagateInsertions(SequenceI profileseq,
+          AlignmentView input);
 }
diff --git a/src/jalview/datamodel/AlignmentOrder.java b/src/jalview/datamodel/AlignmentOrder.java
index 6d09145..ef46d79 100755
--- a/src/jalview/datamodel/AlignmentOrder.java
+++ b/src/jalview/datamodel/AlignmentOrder.java
@@ -80,7 +80,7 @@ public class AlignmentOrder
    */
   public AlignmentOrder(AlignmentI orderFrom)
   {
-    Order = new ArrayList<SequenceI>();
+    Order = new ArrayList<>();
 
     for (SequenceI seq : orderFrom.getSequences())
     {
@@ -96,7 +96,7 @@ public class AlignmentOrder
    */
   public AlignmentOrder(SequenceI[] orderFrom)
   {
-    Order = new ArrayList<SequenceI>(Arrays.asList(orderFrom));
+    Order = new ArrayList<>(Arrays.asList(orderFrom));
   }
 
   /**
diff --git a/src/jalview/datamodel/AnnotatedCollectionI.java b/src/jalview/datamodel/AnnotatedCollectionI.java
index 2963fd5..878f22a 100644
--- a/src/jalview/datamodel/AnnotatedCollectionI.java
+++ b/src/jalview/datamodel/AnnotatedCollectionI.java
@@ -61,4 +61,6 @@ public interface AnnotatedCollectionI extends SequenceCollectionI
    *         alignment, parent group).
    */
   AnnotatedCollectionI getContext();
+
+  
 }
diff --git a/src/jalview/datamodel/CigarArray.java b/src/jalview/datamodel/CigarArray.java
index 1723f1d..17e9ea6 100644
--- a/src/jalview/datamodel/CigarArray.java
+++ b/src/jalview/datamodel/CigarArray.java
@@ -20,7 +20,7 @@
  */
 package jalview.datamodel;
 
-import java.util.List;
+import java.util.Iterator;
 
 public class CigarArray extends CigarBase
 {
@@ -90,9 +90,7 @@ public class CigarArray extends CigarBase
           SequenceGroup selectionGroup)
   {
     this(constructSeqCigarArray(alignment, selectionGroup));
-    constructFromAlignment(alignment,
-            hidden != null ? hidden.getHiddenColumnsCopy() : null,
-            selectionGroup);
+    constructFromAlignment(alignment, hidden, selectionGroup);
   }
 
   private static int[] _calcStartEndBounds(AlignmentI alignment,
@@ -154,33 +152,25 @@ public class CigarArray extends CigarBase
    * @param selectionGroup
    */
   private void constructFromAlignment(AlignmentI alignment,
-          List<int[]> list, SequenceGroup selectionGroup)
+          HiddenColumns hidden, SequenceGroup selectionGroup)
   {
     int[] _startend = _calcStartEndBounds(alignment, selectionGroup);
-    int start = _startend[1], end = _startend[2];
+    int start = _startend[1];
+    int end = _startend[2];
     // now construct the CigarArray operations
-    if (list != null)
+    if (hidden != null)
     {
       int[] region;
-      int hideStart, hideEnd;
+      int hideStart;
+      int hideEnd;
       int last = start;
-      for (int j = 0; last < end & j < list.size(); j++)
+
+      Iterator<int[]> regions = hidden.getBoundedIterator(start, end);
+      while (regions.hasNext())
       {
-        region = list.get(j);
+        region = regions.next();
         hideStart = region[0];
         hideEnd = region[1];
-        // edit hidden regions to selection range
-
-        // just move on if hideEnd is before last
-        if (hideEnd < last)
-        {
-          continue;
-        }
-        // exit if next region is after end
-        if (hideStart > end)
-        {
-          break;
-        }
 
         // truncate region at start if last falls in region
         if ((hideStart < last) && (hideEnd >= last))
@@ -204,6 +194,7 @@ public class CigarArray extends CigarBase
         addOperation(CigarArray.D, 1 + hideEnd - hideStart);
         last = hideEnd + 1;
       }
+
       // Final match if necessary.
       if (last <= end)
       {
diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index 0ac14e5..7a30141 100755
--- a/src/jalview/datamodel/DBRefSource.java
+++ b/src/jalview/datamodel/DBRefSource.java
@@ -96,7 +96,7 @@ public class DBRefSource
    * List of databases whose sequences might have coding regions annotated
    */
   public static final String[] DNACODINGDBS = { EMBL, EMBLCDS, GENEDB,
-      ENSEMBL };
+      ENSEMBL, ENSEMBLGENOMES };
 
   public static final String[] CODINGDBS = { EMBLCDS, GENEDB, ENSEMBL };
 
@@ -105,7 +105,7 @@ public class DBRefSource
 
   public static String[] allSources()
   {
-    List<String> src = new ArrayList<String>();
+    List<String> src = new ArrayList<>();
     for (Field f : DBRefSource.class.getFields())
     {
       if (String.class.equals(f.getType()))
diff --git a/src/jalview/datamodel/HMMNode.java b/src/jalview/datamodel/HMMNode.java
new file mode 100644
index 0000000..b646eee
--- /dev/null
+++ b/src/jalview/datamodel/HMMNode.java
@@ -0,0 +1,148 @@
+package jalview.datamodel;
+
+/**
+ * stores data for each node in the hmm model
+ * @author TZVanaalten
+ *
+ */
+public class HMMNode
+{
+  //contains the match emissions for each symbol 
+  double[] matchEmissions;
+
+  //contains the insert emissions for each symbol 
+  double[] insertEmissions;
+
+  // contains the state transitions for each possible transition. These are mm,
+  // mi, md, im, ii, dm and dd in order
+  double[] stateTransitions;
+  
+  //annotations
+  int residueNumber;
+  char consensusResidue;
+  char referenceAnnotation;
+  char maskValue;
+  char consensusStructure;
+
+  /**
+   * Constructor
+   */
+  public HMMNode()
+  {
+  }
+
+  public double[] getMatchEmissions()
+  {
+    return matchEmissions;
+  }
+
+  double getMatchEmission(int symbolIndex)
+  {
+    return matchEmissions[symbolIndex];
+  }
+
+  public void setMatchEmissions(double[] matches)
+  {
+    this.matchEmissions = matches;
+  }
+
+  public double[] getInsertEmissions()
+  {
+    return insertEmissions;
+  }
+
+  double getInsertEmission(int symbolIndex)
+  {
+    return insertEmissions[symbolIndex];
+  }
+
+  public void setInsertEmissions(double[] insertEmissionsL)
+  {
+    this.insertEmissions = insertEmissionsL;
+  }
+
+  public double[] getStateTransitions()
+  {
+    return stateTransitions;
+  }
+
+  double getStateTransition(int transition)
+  {
+    return stateTransitions[transition];
+  }
+
+  public void setStateTransitions(double[] stateTransitionsM)
+  {
+    this.stateTransitions = stateTransitionsM;
+  }
+
+  int getResidueNumber()
+  {
+    return residueNumber;
+  }
+  public void setResidueNumber(int resNo)
+  {
+    this.residueNumber = resNo;
+  }
+
+  char getConsensusResidue()
+  {
+    return consensusResidue;
+  }
+  public void setConsensusResidue(char consensusResidue)
+  {
+    this.consensusResidue = consensusResidue;
+  }
+
+  char getReferenceAnnotation()
+  {
+    return referenceAnnotation;
+  }
+  public void setReferenceAnnotation(char referenceAnnotation)
+  {
+    this.referenceAnnotation = referenceAnnotation;
+  }
+
+  char getMaskValue()
+  {
+    return maskValue;
+  }
+  public void setMaskValue(char maskValue)
+  {
+    this.maskValue = maskValue;
+  }
+
+  char getConsensusStructure()
+  {
+    return consensusStructure;
+  }
+  public void setConsensusStructure(char consensusStructure)
+  {
+    this.consensusStructure = consensusStructure;
+  }
+
+  /**
+   * Answers the symbol index of the symbol with the highest match emission
+   * probability (first symbol in case of a tie). Note this object stores
+   * probabilities, not the negative logarithms as in the HMM file.
+   * 
+   * @return
+   */
+  int getMaxMatchEmissionIndex()
+  {
+    int maxIndex = 0;
+    double max = 0D;
+
+    for (int i = 0; i < matchEmissions.length; i++)
+    {
+      if (matchEmissions[i] > max)
+      {
+        max = matchEmissions[i];
+        maxIndex = i;
+      }
+    }
+    return maxIndex;
+  }
+}
+   
+  
diff --git a/src/jalview/datamodel/HiddenColumns.java b/src/jalview/datamodel/HiddenColumns.java
index c0a43ee..a7e93da 100644
--- a/src/jalview/datamodel/HiddenColumns.java
+++ b/src/jalview/datamodel/HiddenColumns.java
@@ -20,25 +20,71 @@
  */
 package jalview.datamodel;
 
-import jalview.util.Comparison;
-import jalview.util.ShiftList;
-
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.BitSet;
-import java.util.Collections;
+import java.util.Iterator;
 import java.util.List;
-import java.util.Vector;
 import java.util.concurrent.locks.ReentrantReadWriteLock;
 
+/**
+ * This class manages the collection of hidden columns associated with an
+ * alignment. To iterate over the collection, or over visible columns/regions,
+ * use an iterator obtained from one of:
+ * 
+ * - getBoundedIterator: iterates over the hidden regions, within some bounds,
+ * returning *absolute* positions
+ * 
+ * - getBoundedStartIterator: iterates over the start positions of hidden
+ * regions, within some bounds, returning *visible* positions
+ * 
+ * - getVisContigsIterator: iterates over visible regions in a range, returning
+ * *absolute* positions
+ * 
+ * - getVisibleColsIterator: iterates over the visible *columns*
+ * 
+ * For performance reasons, provide bounds where possible. Note that column
+ * numbering begins at 0 throughout this class.
+ * 
+ * @author kmourao
+ */
+
+/* Implementation notes:
+ * 
+ * Methods which change the hiddenColumns collection should use a writeLock to
+ * prevent other threads accessing the hiddenColumns collection while changes
+ * are being made. They should also reset the hidden columns cursor, and either
+ * update the hidden columns count, or set it to 0 (so that it will later be
+ * updated when needed).
+ * 
+ * 
+ * Methods which only need read access to the hidden columns collection should
+ * use a readLock to prevent other threads changing the hidden columns
+ * collection while it is in use.
+ */
 public class HiddenColumns
 {
+  private static final int HASH_MULTIPLIER = 31;
+
   private static final ReentrantReadWriteLock LOCK = new ReentrantReadWriteLock();
 
   /*
+   * Cursor which tracks the last used hidden columns region, and the number 
+   * of hidden columns up to (but not including) that region.
+   */
+  private HiddenColumnsCursor cursor = new HiddenColumnsCursor();
+
+  /*
+   * cache of the number of hidden columns: must be kept up to date by methods 
+   * which add or remove hidden columns
+   */
+  private int numColumns = 0;
+
+  /*
    * list of hidden column [start, end] ranges; the list is maintained in
    * ascending start column order
    */
-  private ArrayList<int[]> hiddenColumns;
+  private List<int[]> hiddenColumns = new ArrayList<>();
 
   /**
    * Constructor
@@ -51,19 +97,263 @@ public class HiddenColumns
    * Copy constructor
    * 
    * @param copy
+   *          the HiddenColumns object to copy from
    */
   public HiddenColumns(HiddenColumns copy)
   {
+    this(copy, Integer.MIN_VALUE, Integer.MAX_VALUE, 0);
+  }
+
+  /**
+   * Copy constructor within bounds and with offset. Copies hidden column
+   * regions fully contained between start and end, and offsets positions by
+   * subtracting offset.
+   * 
+   * @param copy
+   *          HiddenColumns instance to copy from
+   * @param start
+   *          lower bound to copy from
+   * @param end
+   *          upper bound to copy to
+   * @param offset
+   *          offset to subtract from each region boundary position
+   * 
+   */
+  public HiddenColumns(HiddenColumns copy, int start, int end, int offset)
+  {
     try
     {
       LOCK.writeLock().lock();
       if (copy != null)
       {
-        if (copy.hiddenColumns != null)
+        numColumns = 0;
+        Iterator<int[]> it = copy.getBoundedIterator(start, end);
+        while (it.hasNext())
+        {
+          int[] region = it.next();
+          // still need to check boundaries because iterator returns
+          // all overlapping regions and we need contained regions
+          if (region[0] >= start && region[1] <= end)
+          {
+            hiddenColumns.add(
+                    new int[]
+            { region[0] - offset, region[1] - offset });
+            numColumns += region[1] - region[0] + 1;
+          }
+        }
+        cursor = new HiddenColumnsCursor(hiddenColumns);
+      }
+    } finally
+    {
+      LOCK.writeLock().unlock();
+    }
+  }
+
+  /**
+   * Adds the specified column range to the hidden columns collection
+   * 
+   * @param start
+   *          start of range to add (absolute position in alignment)
+   * @param end
+   *          end of range to add (absolute position in alignment)
+   */
+  public void hideColumns(int start, int end)
+  {
+    try
+    {
+      LOCK.writeLock().lock();
+
+      int previndex = 0;
+      int prevHiddenCount = 0;
+      int regionindex = 0;
+      if (!hiddenColumns.isEmpty())
+      {
+        // set up cursor reset values
+        HiddenCursorPosition cursorPos = cursor.findRegionForColumn(start, false);
+        regionindex = cursorPos.getRegionIndex();
+
+        if (regionindex > 0)
+        {
+          // get previous index and hidden count for updating the cursor later
+          previndex = regionindex - 1;
+          int[] prevRegion = hiddenColumns.get(previndex);
+          prevHiddenCount = cursorPos.getHiddenSoFar()
+                  - (prevRegion[1] - prevRegion[0] + 1);
+        }
+      }
+
+      // new range follows everything else; check first to avoid looping over
+      // whole hiddenColumns collection
+      if (hiddenColumns.isEmpty()
+              || start > hiddenColumns.get(hiddenColumns.size() - 1)[1])
+      {
+        hiddenColumns.add(new int[] { start, end });
+        numColumns += end - start + 1;
+      }
+      else
+      {
+        /*
+         * traverse existing hidden ranges and insert / amend / append as
+         * appropriate
+         */
+        boolean added = false;
+        if (regionindex > 0)
+        {
+          added = insertRangeAtRegion(regionindex - 1, start, end);
+        }
+        if (!added && regionindex < hiddenColumns.size())
+        {
+          insertRangeAtRegion(regionindex, start, end);
+        }
+      }
+
+      // reset the cursor to just before our insertion point: this saves
+      // a lot of reprocessing in large alignments
+      cursor = new HiddenColumnsCursor(hiddenColumns, previndex,
+              prevHiddenCount);
+    } finally
+    {
+      LOCK.writeLock().unlock();
+    }
+  }
+
+  /**
+   * Insert [start, range] at the region at index i in hiddenColumns, if
+   * feasible
+   * 
+   * @param i
+   *          index to insert at
+   * @param start
+   *          start of range to insert
+   * @param end
+   *          end of range to insert
+   * @return true if range was successfully inserted
+   */
+  private boolean insertRangeAtRegion(int i, int start, int end)
+  {
+    boolean added = false;
+
+    int[] region = hiddenColumns.get(i);
+    if (end < region[0] - 1)
+    {
+      /*
+       * insert discontiguous preceding range
+       */
+      hiddenColumns.add(i, new int[] { start, end });
+      numColumns += end - start + 1;
+      added = true;
+    }
+    else if (end <= region[1])
+    {
+      /*
+       * new range overlaps existing, or is contiguous preceding it - adjust
+       * start column
+       */
+      int oldstart = region[0];
+      region[0] = Math.min(region[0], start);
+      numColumns += oldstart - region[0]; // new columns are between old and
+                                              // adjusted starts
+      added = true;
+    }
+    else if (start <= region[1] + 1)
+    {
+      /*
+       * new range overlaps existing, or is contiguous following it - adjust
+       * start and end columns
+       */
+      insertRangeAtOverlap(i, start, end, region);
+      added = true;
+    }
+    return added;
+  }
+
+  /**
+   * Insert a range whose start position overlaps an existing region and/or is
+   * contiguous to the right of the region
+   * 
+   * @param i
+   *          index to insert at
+   * @param start
+   *          start of range to insert
+   * @param end
+   *          end of range to insert
+   * @param region
+   *          the overlapped/continued region
+   */
+  private void insertRangeAtOverlap(int i, int start, int end, int[] region)
+  {
+    int oldstart = region[0];
+    int oldend = region[1];
+    region[0] = Math.min(region[0], start);
+    region[1] = Math.max(region[1], end);
+
+    numColumns += oldstart - region[0];
+
+    /*
+     * also update or remove any subsequent ranges 
+     * that are overlapped
+     */
+    int endi = i;
+    while (endi < hiddenColumns.size() - 1)
+    {
+      int[] nextRegion = hiddenColumns.get(endi + 1);
+      if (nextRegion[0] > end + 1)
+      {
+        /*
+         * gap to next hidden range - no more to update
+         */
+        break;
+      }
+      numColumns -= nextRegion[1] - nextRegion[0] + 1;
+      region[1] = Math.max(nextRegion[1], end);
+      endi++;
+    }
+    numColumns += region[1] - oldend;
+    hiddenColumns.subList(i + 1, endi + 1).clear();
+  }
+
+  /**
+   * hide a list of ranges
+   * 
+   * @param ranges
+   */
+  public void hideList(List<int[]> ranges)
+  {
+    try
+    {
+      LOCK.writeLock().lock();
+      for (int[] r : ranges)
+      {
+        hideColumns(r[0], r[1]);
+      }
+      cursor = new HiddenColumnsCursor(hiddenColumns);
+
+    } finally
+    {
+      LOCK.writeLock().unlock();
+    }
+  }
+
+  /**
+   * Unhides, and adds to the selection list, all hidden columns
+   */
+  public void revealAllHiddenColumns(ColumnSelection sel)
+  {
+    try
+    {
+      LOCK.writeLock().lock();
+
+      for (int[] region : hiddenColumns)
+      {
+        for (int j = region[0]; j < region[1] + 1; j++)
         {
-          hiddenColumns = copy.copyHiddenRegionsToArrayList();
+          sel.addElement(j);
         }
       }
+      hiddenColumns.clear();
+      cursor = new HiddenColumnsCursor(hiddenColumns);
+      numColumns = 0;
+
     } finally
     {
       LOCK.writeLock().unlock();
@@ -71,16 +361,46 @@ public class HiddenColumns
   }
 
   /**
-   * This method is used to return all the HiddenColumn regions and is intended
-   * to remain private. External callers which need a copy of the regions can
-   * call getHiddenColumnsCopyAsList.
+   * Reveals, and marks as selected, the hidden column range with the given
+   * start column
    * 
-   * @return empty list or List of hidden column intervals
+   * @param start
+   *          the start column to look for
+   * @param sel
+   *          the column selection to add the hidden column range to
    */
-  private List<int[]> getHiddenRegions()
+  public void revealHiddenColumns(int start, ColumnSelection sel)
   {
-    return hiddenColumns == null ? Collections.<int[]> emptyList()
-            : hiddenColumns;
+    try
+    {
+      LOCK.writeLock().lock();
+
+      if (!hiddenColumns.isEmpty())
+      {
+        int regionIndex = cursor.findRegionForColumn(start, false)
+                .getRegionIndex();
+
+        if (regionIndex != -1 && regionIndex != hiddenColumns.size())
+        {
+          // regionIndex is the region which either contains start
+          // or lies to the right of start
+          int[] region = hiddenColumns.get(regionIndex);
+          if (start == region[0])
+          {
+            for (int j = region[0]; j < region[1] + 1; j++)
+            {
+              sel.addElement(j);
+            }
+            int colsToRemove = region[1] - region[0] + 1;
+            hiddenColumns.remove(regionIndex);
+            numColumns -= colsToRemove;
+          }
+        }
+      }
+    } finally
+    {
+      LOCK.writeLock().unlock();
+    }
   }
 
   /**
@@ -99,16 +419,22 @@ public class HiddenColumns
     {
       LOCK.readLock().lock();
       StringBuilder regionBuilder = new StringBuilder();
-      if (hiddenColumns != null)
+
+      boolean first = true;
+      for (int[] range : hiddenColumns)
       {
-        for (int[] range : hiddenColumns)
+        if (!first)
+        {
+          regionBuilder.append(delimiter);
+        }
+        else
         {
-          regionBuilder.append(delimiter).append(range[0]).append(between)
-                  .append(range[1]);
+          first = false;
         }
+        regionBuilder.append(range[0]).append(between).append(range[1]);
 
-        regionBuilder.deleteCharAt(0);
       }
+
       return regionBuilder.toString();
     } finally
     {
@@ -123,18 +449,20 @@ public class HiddenColumns
    */
   public int getSize()
   {
+    return numColumns;
+  }
+
+  /**
+   * Get the number of distinct hidden regions
+   * 
+   * @return number of regions
+   */
+  public int getNumberOfRegions()
+  {
     try
     {
       LOCK.readLock().lock();
-      int size = 0;
-      if (hasHiddenColumns())
-      {
-        for (int[] range : hiddenColumns)
-        {
-          size += range[1] - range[0] + 1;
-        }
-      }
-      return size;
+      return hiddenColumns.size();
     } finally
     {
       LOCK.readLock().unlock();
@@ -157,25 +485,23 @@ public class HiddenColumns
       /*
        * check hidden columns are either both null, or match
        */
-      if (this.hiddenColumns == null)
-      {
-        return (that.hiddenColumns == null);
-      }
-      if (that.hiddenColumns == null
-              || that.hiddenColumns.size() != this.hiddenColumns.size())
+
+      if (that.hiddenColumns.size() != this.hiddenColumns.size())
       {
         return false;
       }
-      int i = 0;
-      for (int[] thisRange : hiddenColumns)
+
+      Iterator<int[]> it = this.iterator();
+      Iterator<int[]> thatit = that.iterator();
+      while (it.hasNext())
       {
-        int[] thatRange = that.hiddenColumns.get(i++);
-        if (thisRange[0] != thatRange[0] || thisRange[1] != thatRange[1])
+        if (!(Arrays.equals(it.next(), thatit.next())))
         {
           return false;
         }
       }
       return true;
+
     } finally
     {
       LOCK.readLock().unlock();
@@ -189,23 +515,19 @@ public class HiddenColumns
    *          int column index in alignment view (count from zero)
    * @return alignment column index for column
    */
-  public int adjustForHiddenColumns(int column)
+  public int visibleToAbsoluteColumn(int column)
   {
     try
     {
       LOCK.readLock().lock();
       int result = column;
-      if (hiddenColumns != null)
+
+      if (!hiddenColumns.isEmpty())
       {
-        for (int i = 0; i < hiddenColumns.size(); i++)
-        {
-          int[] region = hiddenColumns.get(i);
-          if (result >= region[0])
-          {
-            result += region[1] - region[0] + 1;
-          }
-        }
+        result += cursor.findRegionForColumn(column, true)
+                .getHiddenSoFar();
       }
+
       return result;
     } finally
     {
@@ -216,54 +538,52 @@ public class HiddenColumns
   /**
    * Use this method to find out where a column will appear in the visible
    * alignment when hidden columns exist. If the column is not visible, then the
-   * left-most visible column will always be returned.
+   * index of the next visible column on the left will be returned (or 0 if
+   * there is no visible column on the left)
    * 
    * @param hiddenColumn
    *          the column index in the full alignment including hidden columns
    * @return the position of the column in the visible alignment
    */
-  public int findColumnPosition(int hiddenColumn)
+  public int absoluteToVisibleColumn(int hiddenColumn)
   {
     try
     {
       LOCK.readLock().lock();
       int result = hiddenColumn;
-      if (hiddenColumns != null)
-      {
-        int index = 0;
-        int[] region;
-        do
-        {
-          region = hiddenColumns.get(index++);
-          if (hiddenColumn > region[1])
-          {
-            result -= region[1] + 1 - region[0];
-          }
-        } while ((hiddenColumn > region[1])
-                && (index < hiddenColumns.size()));
 
-        if (hiddenColumn >= region[0] && hiddenColumn <= region[1])
+      if (!hiddenColumns.isEmpty())
+      {
+        HiddenCursorPosition cursorPos = cursor
+                .findRegionForColumn(hiddenColumn, false);
+        int index = cursorPos.getRegionIndex();
+        int hiddenBeforeCol = cursorPos.getHiddenSoFar();
+    
+        // just subtract hidden cols count - this works fine if column is
+        // visible
+        result = hiddenColumn - hiddenBeforeCol;
+    
+        // now check in case column is hidden - it will be in the returned
+        // hidden region
+        if (index < hiddenColumns.size())
         {
-          // Here the hidden column is within a region, so
-          // we want to return the position of region[0]-1, adjusted for any
-          // earlier hidden columns.
-          // Calculate the difference between the actual hidden col position
-          // and region[0]-1, and then subtract from result to convert result
-          // from
-          // the adjusted hiddenColumn value to the adjusted region[0]-1 value
-
-          // However, if the region begins at 0 we cannot return region[0]-1
-          // just return 0
-          if (region[0] == 0)
-          {
-            return 0;
-          }
-          else
+          int[] region = hiddenColumns.get(index);
+          if (hiddenColumn >= region[0] && hiddenColumn <= region[1])
           {
-            return result - (hiddenColumn - region[0] + 1);
+            // actually col is hidden, return region[0]-1
+            // unless region[0]==0 in which case return 0
+            if (region[0] == 0)
+            {
+              result = 0;
+            }
+            else
+            {
+              result = region[0] - 1 - hiddenBeforeCol;
+            }
           }
         }
       }
+
       return result; // return the shifted position after removing hidden
                      // columns.
     } finally
@@ -274,113 +594,75 @@ public class HiddenColumns
 
   /**
    * Find the visible column which is a given visible number of columns to the
-   * left of another visible column. i.e. for a startColumn x, the column which
-   * is distance 1 away will be column x-1.
+   * left (negative visibleDistance) or right (positive visibleDistance) of
+   * startColumn. If startColumn is not visible, we use the visible column at
+   * the left boundary of the hidden region containing startColumn.
    * 
    * @param visibleDistance
-   *          the number of visible columns to offset by
+   *          the number of visible columns to offset by (left offset = negative
+   *          value; right offset = positive value)
    * @param startColumn
-   *          the column to start from
-   * @return the position of the column in the visible alignment
+   *          the position of the column to start from (absolute position)
+   * @return the position of the column which is <visibleDistance> away
+   *         (absolute position)
    */
-  public int subtractVisibleColumns(int visibleDistance, int startColumn)
+  public int offsetByVisibleColumns(int visibleDistance, int startColumn)
   {
     try
     {
-
       LOCK.readLock().lock();
-      int distance = visibleDistance;
-
-      // in case startColumn is in a hidden region, move it to the left
-      int start = adjustForHiddenColumns(findColumnPosition(startColumn));
-
-      // get index of hidden region to left of start
-      int index = getHiddenIndexLeft(start);
-      if (index == -1)
-      {
-        // no hidden regions to left of startColumn
-        return start - distance;
-      }
-
-      // walk backwards through the alignment subtracting the counts of visible
-      // columns from distance
-      int[] region;
-      int gap = 0;
-      int nextstart = start;
-
-      while ((index > -1) && (distance - gap > 0))
-      {
-        // subtract the gap to right of region from distance
-        distance -= gap;
-        start = nextstart;
-
-        // calculate the next gap
-        region = hiddenColumns.get(index);
-        gap = start - region[1];
-
-        // set start to just to left of current region
-        nextstart = region[0] - 1;
-        index--;
-      }
+      int start = absoluteToVisibleColumn(startColumn);
+      return visibleToAbsoluteColumn(start + visibleDistance);
 
-      if (distance - gap > 0)
-      {
-        // fell out of loop because there are no more hidden regions
-        distance -= gap;
-        return nextstart - distance;
-      }
-      return start - distance;
     } finally
     {
       LOCK.readLock().unlock();
     }
-
   }
 
   /**
-   * Use this method to determine the set of hiddenRegion start positions
+   * This method returns the rightmost limit of a region of an alignment with
+   * hidden columns. In otherwords, the next hidden column.
    * 
-   * @return list of column number in visible view where hidden regions start
+   * @param alPos
+   *          the absolute (visible) alignmentPosition to find the next hidden
+   *          column for
+   * @return the index of the next hidden column, or alPos if there is no next
+   *         hidden column
    */
-  public List<Integer> findHiddenRegionPositions()
+  public int getNextHiddenBoundary(boolean left, int alPos)
   {
     try
     {
       LOCK.readLock().lock();
-      List<Integer> positions = null;
-
-      if (hiddenColumns != null)
+      if (!hiddenColumns.isEmpty())
       {
-        positions = new ArrayList<>(hiddenColumns.size());
+        int index = cursor.findRegionForColumn(alPos, false)
+                .getRegionIndex();
 
-        positions.add(hiddenColumns.get(0)[0]);
-        for (int i = 1; i < hiddenColumns.size(); ++i)
+        if (left && index > 0)
         {
-
-          int result = 0;
-          if (hiddenColumns != null)
+          int[] region = hiddenColumns.get(index - 1);
+          return region[1];
+        }
+        else if (!left && index < hiddenColumns.size())
+        {
+          int[] region = hiddenColumns.get(index);
+          if (alPos < region[0])
           {
-            int index = 0;
-            int gaps = 0;
-            do
-            {
-              int[] region = hiddenColumns.get(index);
-              gaps += region[1] + 1 - region[0];
-              result = region[1] + 1;
-              index++;
-            } while (index <= i);
-
-            result -= gaps;
+            return region[0];
+          }
+          else if ((alPos <= region[1])
+                  && (index + 1 < hiddenColumns.size()))
+          {
+            // alPos is within a hidden region, return the next one
+            // if there is one
+            region = hiddenColumns.get(index + 1);
+            return region[0];
           }
-          positions.add(result);
         }
       }
-      else
-      {
-        positions = new ArrayList<>();
-      }
-
-      return positions;
+      return alPos;
     } finally
     {
       LOCK.readLock().unlock();
@@ -388,69 +670,54 @@ public class HiddenColumns
   }
 
   /**
-   * This method returns the rightmost limit of a region of an alignment with
-   * hidden columns. In otherwords, the next hidden column.
+   * Answers if a column in the alignment is visible
    * 
-   * @param index
-   *          int
+   * @param column
+   *          absolute position of column in the alignment
+   * @return true if column is visible
    */
-  public int getHiddenBoundaryRight(int alPos)
+  public boolean isVisible(int column)
   {
     try
     {
       LOCK.readLock().lock();
-      if (hiddenColumns != null)
+
+      if (!hiddenColumns.isEmpty())
       {
-        int index = 0;
-        do
+        int regionindex = cursor.findRegionForColumn(column, false)
+                .getRegionIndex();
+        if (regionindex > -1 && regionindex < hiddenColumns.size())
         {
-          int[] region = hiddenColumns.get(index);
-          if (alPos < region[0])
+          int[] region = hiddenColumns.get(regionindex);
+          // already know that column <= region[1] as cursor returns containing
+          // region or region to right
+          if (column >= region[0])
           {
-            return region[0];
+            return false;
           }
-
-          index++;
-        } while (index < hiddenColumns.size());
+        }
       }
+      return true;
 
-      return alPos;
     } finally
     {
       LOCK.readLock().unlock();
     }
-
   }
 
   /**
-   * This method returns the leftmost limit of a region of an alignment with
-   * hidden columns. In otherwords, the previous hidden column.
    * 
-   * @param index
-   *          int
+   * @return true if there are columns hidden
    */
-  public int getHiddenBoundaryLeft(int alPos)
+  public boolean hasHiddenColumns()
   {
     try
     {
       LOCK.readLock().lock();
 
-      if (hiddenColumns != null)
-      {
-        int index = hiddenColumns.size() - 1;
-        do
-        {
-          int[] region = hiddenColumns.get(index);
-          if (alPos > region[1])
-          {
-            return region[1];
-          }
-
-          index--;
-        } while (index > -1);
-      }
-
-      return alPos;
+      // we don't use getSize()>0 here because it has to iterate over
+      // the full hiddenColumns collection and so will be much slower
+      return (!hiddenColumns.isEmpty());
     } finally
     {
       LOCK.readLock().unlock();
@@ -458,258 +725,169 @@ public class HiddenColumns
   }
 
   /**
-   * This method returns the index of the hidden region to the left of a column
-   * position. If the column is in a hidden region it returns the index of the
-   * region to the left. If there is no hidden region to the left it returns -1.
    * 
-   * @param pos
-   *          int
+   * @return true if there is more than one hidden column region
    */
-  private int getHiddenIndexLeft(int pos)
+  public boolean hasMultiHiddenColumnRegions()
   {
     try
     {
-
       LOCK.readLock().lock();
-      if (hiddenColumns != null)
-      {
-        int index = hiddenColumns.size() - 1;
-        do
-        {
-          int[] region = hiddenColumns.get(index);
-          if (pos > region[1])
-          {
-            return index;
-          }
-
-          index--;
-        } while (index > -1);
-      }
-
-      return -1;
+      return !hiddenColumns.isEmpty() && hiddenColumns.size() > 1;
     } finally
     {
       LOCK.readLock().unlock();
     }
-
   }
 
+
   /**
-   * Adds the specified column range to the hidden columns
-   * 
-   * @param start
-   * @param end
+   * Returns a hashCode built from hidden column ranges
    */
-  public void hideColumns(int start, int end)
+  @Override
+  public int hashCode()
   {
-    boolean wasAlreadyLocked = false;
     try
     {
-      // check if the write lock was already locked by this thread,
-      // as this method can be called internally in loops within HiddenColumns
-      if (!LOCK.isWriteLockedByCurrentThread())
-      {
-        LOCK.writeLock().lock();
-      }
-      else
-      {
-        wasAlreadyLocked = true;
-      }
-
-      if (hiddenColumns == null)
-      {
-        hiddenColumns = new ArrayList<>();
-      }
+      LOCK.readLock().lock();
+      int hashCode = 1;
 
-      /*
-       * traverse existing hidden ranges and insert / amend / append as
-       * appropriate
-       */
-      for (int i = 0; i < hiddenColumns.size(); i++)
+      for (int[] hidden : hiddenColumns)
       {
-        int[] region = hiddenColumns.get(i);
-
-        if (end < region[0] - 1)
-        {
-          /*
-           * insert discontiguous preceding range
-           */
-          hiddenColumns.add(i, new int[] { start, end });
-          return;
-        }
-
-        if (end <= region[1])
-        {
-          /*
-           * new range overlaps existing, or is contiguous preceding it - adjust
-           * start column
-           */
-          region[0] = Math.min(region[0], start);
-          return;
-        }
-
-        if (start <= region[1] + 1)
-        {
-          /*
-           * new range overlaps existing, or is contiguous following it - adjust
-           * start and end columns
-           */
-          region[0] = Math.min(region[0], start);
-          region[1] = Math.max(region[1], end);
-
-          /*
-           * also update or remove any subsequent ranges 
-           * that are overlapped
-           */
-          while (i < hiddenColumns.size() - 1)
-          {
-            int[] nextRegion = hiddenColumns.get(i + 1);
-            if (nextRegion[0] > end + 1)
-            {
-              /*
-               * gap to next hidden range - no more to update
-               */
-              break;
-            }
-            region[1] = Math.max(nextRegion[1], end);
-            hiddenColumns.remove(i + 1);
-          }
-          return;
-        }
+        hashCode = HASH_MULTIPLIER * hashCode + hidden[0];
+        hashCode = HASH_MULTIPLIER * hashCode + hidden[1];
       }
-
-      /*
-       * remaining case is that the new range follows everything else
-       */
-      hiddenColumns.add(new int[] { start, end });
+      return hashCode;
     } finally
     {
-      if (!wasAlreadyLocked)
-      {
-        LOCK.writeLock().unlock();
-      }
+      LOCK.readLock().unlock();
     }
   }
 
-  public boolean isVisible(int column)
+  /**
+   * Hide columns corresponding to the marked bits
+   * 
+   * @param inserts
+   *          - columns mapped to bits starting from zero
+   */
+  public void hideColumns(BitSet inserts)
+  {
+    hideColumns(inserts, 0, inserts.length() - 1);
+  }
+
+  /**
+   * Hide columns corresponding to the marked bits, within the range
+   * [start,end]. Entries in tohide which are outside [start,end] are ignored.
+   * 
+   * @param tohide
+   *          columns mapped to bits starting from zero
+   * @param start
+   *          start of range to hide columns within
+   * @param end
+   *          end of range to hide columns within
+   */
+  private void hideColumns(BitSet tohide, int start, int end)
   {
     try
     {
-      LOCK.readLock().lock();
-
-      if (hiddenColumns != null)
+      LOCK.writeLock().lock();
+      for (int firstSet = tohide
+              .nextSetBit(start), lastSet = start; firstSet >= start
+                      && lastSet <= end; firstSet = tohide
+                      .nextSetBit(lastSet))
       {
-        for (int[] region : hiddenColumns)
+        lastSet = tohide.nextClearBit(firstSet);
+        if (lastSet <= end)
         {
-          if (column >= region[0] && column <= region[1])
-          {
-            return false;
-          }
+          hideColumns(firstSet, lastSet - 1);
+        }
+        else if (firstSet <= end)
+        {
+          hideColumns(firstSet, end);
         }
       }
-
-      return true;
+      cursor = new HiddenColumnsCursor(hiddenColumns);
     } finally
     {
-      LOCK.readLock().unlock();
-    }
-  }
-
-  private ArrayList<int[]> copyHiddenRegionsToArrayList()
-  {
-    int size = 0;
-    if (hiddenColumns != null)
-    {
-      size = hiddenColumns.size();
-    }
-    ArrayList<int[]> copy = new ArrayList<>(size);
-
-    for (int i = 0, j = size; i < j; i++)
-    {
-      int[] rh;
-      int[] cp;
-      rh = hiddenColumns.get(i);
-      if (rh != null)
-      {
-        cp = new int[rh.length];
-        System.arraycopy(rh, 0, cp, 0, rh.length);
-        copy.add(cp);
-      }
+      LOCK.writeLock().unlock();
     }
-
-    return copy;
   }
 
   /**
-   * Returns a copy of the vector of hidden regions, as an ArrayList. Before
-   * using this method please consider if you really need access to the hidden
-   * regions - a new (or existing!) method on HiddenColumns might be more
-   * appropriate.
+   * Hide columns corresponding to the marked bits, within the range
+   * [start,end]. Entries in tohide which are outside [start,end] are ignored.
+   * NB Existing entries in [start,end] are cleared.
    * 
-   * @return hidden regions as an ArrayList of [start,end] pairs
+   * @param tohide
+   *          columns mapped to bits starting from zero
+   * @param start
+   *          start of range to hide columns within
+   * @param end
+   *          end of range to hide columns within
    */
-  public ArrayList<int[]> getHiddenColumnsCopy()
+  public void clearAndHideColumns(BitSet tohide, int start, int end)
   {
-    try
-    {
-      LOCK.readLock().lock();
-      return copyHiddenRegionsToArrayList();
-    } finally
-    {
-      LOCK.readLock().unlock();
-    }
+    clearHiddenColumnsInRange(start, end);
+    hideColumns(tohide, start, end);
   }
 
   /**
-   * propagate shift in alignment columns to column selection
+   * Make all columns in the range [start,end] visible
    * 
    * @param start
-   *          beginning of edit
-   * @param left
-   *          shift in edit (+ve for removal, or -ve for inserts)
+   *          start of range to show columns
+   * @param end
+   *          end of range to show columns
    */
-  public List<int[]> compensateForEdit(int start, int change,
-          ColumnSelection sel)
+  private void clearHiddenColumnsInRange(int start, int end)
   {
     try
     {
       LOCK.writeLock().lock();
-      List<int[]> deletedHiddenColumns = null;
-
-      if (hiddenColumns != null)
+      
+      if (!hiddenColumns.isEmpty())
       {
-        deletedHiddenColumns = new ArrayList<>();
-        int hSize = hiddenColumns.size();
-        for (int i = 0; i < hSize; i++)
+        HiddenCursorPosition pos = cursor.findRegionForColumn(start, false);
+        int index = pos.getRegionIndex();
+
+        if (index != -1 && index != hiddenColumns.size())
         {
-          int[] region = hiddenColumns.get(i);
-          if (region[0] > start && start + change > region[1])
+          // regionIndex is the region which either contains start
+          // or lies to the right of start
+          int[] region = hiddenColumns.get(index);
+          if (region[0] < start && region[1] >= start)
           {
-            deletedHiddenColumns.add(region);
-
-            hiddenColumns.remove(i);
-            i--;
-            hSize--;
-            continue;
+            // region contains start, truncate so that it ends just before start
+            numColumns -= region[1] - start + 1;
+            region[1] = start - 1;
+            index++;
           }
 
-          if (region[0] > start)
+          int endi = index;
+          while (endi < hiddenColumns.size())
           {
-            region[0] -= change;
-            region[1] -= change;
-          }
+            region = hiddenColumns.get(endi);
 
-          if (region[0] < 0)
-          {
-            region[0] = 0;
+            if (region[1] > end)
+            {
+              if (region[0] <= end)
+              {
+                // region contains end, truncate so it starts just after end
+                numColumns -= end - region[0] + 1;
+                region[0] = end + 1;
+              }
+              break;
+            }
+
+            numColumns -= region[1] - region[0] + 1;
+            endi++;
           }
+          hiddenColumns.subList(index, endi).clear();
 
         }
 
-        this.revealHiddenColumns(0, sel);
+        cursor = new HiddenColumnsCursor(hiddenColumns);
       }
-
-      return deletedHiddenColumns;
     } finally
     {
       LOCK.writeLock().unlock();
@@ -717,47 +895,24 @@ public class HiddenColumns
   }
 
   /**
-   * propagate shift in alignment columns to column selection special version of
-   * compensateForEdit - allowing for edits within hidden regions
    * 
-   * @param start
-   *          beginning of edit
-   * @param left
-   *          shift in edit (+ve for removal, or -ve for inserts)
+   * @param updates
+   *          BitSet where hidden columns will be marked
    */
-  public void compensateForDelEdits(int start, int change)
+  protected void andNot(BitSet updates)
   {
     try
     {
       LOCK.writeLock().lock();
-      if (hiddenColumns != null)
-      {
-        for (int i = 0; i < hiddenColumns.size(); i++)
-        {
-          int[] region = hiddenColumns.get(i);
-          if (region[0] >= start)
-          {
-            region[0] -= change;
-          }
-          if (region[1] >= start)
-          {
-            region[1] -= change;
-          }
-          if (region[1] < region[0])
-          {
-            hiddenColumns.remove(i--);
-          }
 
-          if (region[0] < 0)
-          {
-            region[0] = 0;
-          }
-          if (region[1] < 0)
-          {
-            region[1] = 0;
-          }
-        }
+      BitSet hiddenBitSet = new BitSet();
+      for (int[] range : hiddenColumns)
+      {
+        hiddenBitSet.set(range[0], range[1] + 1);
       }
+      hiddenBitSet.andNot(updates);
+      hiddenColumns.clear();
+      hideColumns(hiddenBitSet);
     } finally
     {
       LOCK.writeLock().unlock();
@@ -765,135 +920,80 @@ public class HiddenColumns
   }
 
   /**
-   * return all visible segments between the given start and end boundaries
+   * Calculate the visible start and end index of an alignment.
    * 
-   * @param start
-   *          (first column inclusive from 0)
-   * @param end
-   *          (last column - not inclusive)
-   * @return int[] {i_start, i_end, ..} where intervals lie in
-   *         start<=i_start<=i_end<end
+   * @param width
+   *          full alignment width
+   * @return integer array where: int[0] = startIndex, and int[1] = endIndex
    */
-  public int[] getVisibleContigs(int start, int end)
+  public int[] getVisibleStartAndEndIndex(int width)
   {
     try
     {
       LOCK.readLock().lock();
-      if (hiddenColumns != null && hiddenColumns.size() > 0)
-      {
-        List<int[]> visiblecontigs = new ArrayList<>();
-        List<int[]> regions = getHiddenRegions();
 
-        int vstart = start;
-        int[] region;
-        int hideStart;
-        int hideEnd;
+      int firstVisible = 0;
+      int lastVisible = width - 1;
 
-        for (int j = 0; vstart < end && j < regions.size(); j++)
-        {
-          region = regions.get(j);
-          hideStart = region[0];
-          hideEnd = region[1];
-
-          if (hideEnd < vstart)
-          {
-            continue;
-          }
-          if (hideStart > vstart)
-          {
-            visiblecontigs.add(new int[] { vstart, hideStart - 1 });
-          }
-          vstart = hideEnd + 1;
-        }
+      if (!hiddenColumns.isEmpty())
+      {
+        // first visible col with index 0, convert to absolute index
+        firstVisible = visibleToAbsoluteColumn(0);
 
-        if (vstart < end)
+        // last visible column is either immediately to left of
+        // last hidden region, or is just the last column in the alignment
+        int[] lastregion = hiddenColumns.get(hiddenColumns.size() - 1);
+        if (lastregion[1] == width - 1)
         {
-          visiblecontigs.add(new int[] { vstart, end - 1 });
+          // last region is at very end of alignment
+          // last visible column immediately precedes it
+          lastVisible = lastregion[0] - 1;
         }
-        int[] vcontigs = new int[visiblecontigs.size() * 2];
-        for (int i = 0, j = visiblecontigs.size(); i < j; i++)
-        {
-          int[] vc = visiblecontigs.get(i);
-          visiblecontigs.set(i, null);
-          vcontigs[i * 2] = vc[0];
-          vcontigs[i * 2 + 1] = vc[1];
-        }
-        visiblecontigs.clear();
-        return vcontigs;
-      }
-      else
-      {
-        return new int[] { start, end - 1 };
       }
+      return new int[] { firstVisible, lastVisible };
+
     } finally
     {
       LOCK.readLock().unlock();
     }
   }
 
-  public String[] getVisibleSequenceStrings(int start, int end,
-          SequenceI[] seqs)
+  /**
+   * Finds the hidden region (if any) which starts or ends at res
+   * 
+   * @param res
+   *          visible residue position, unadjusted for hidden columns
+   * @return region as [start,end] or null if no matching region is found. If
+   *         res is adjacent to two regions, returns the left region.
+   */
+  public int[] getRegionWithEdgeAtRes(int res)
   {
     try
     {
       LOCK.readLock().lock();
-      int iSize = seqs.length;
-      String[] selections = new String[iSize];
-      if (hiddenColumns != null && hiddenColumns.size() > 0)
-      {
-        for (int i = 0; i < iSize; i++)
-        {
-          StringBuffer visibleSeq = new StringBuffer();
-          List<int[]> regions = getHiddenRegions();
-
-          int blockStart = start;
-          int blockEnd = end;
-          int[] region;
-          int hideStart;
-          int hideEnd;
+      int adjres = visibleToAbsoluteColumn(res);
 
-          for (int j = 0; j < regions.size(); j++)
-          {
-            region = regions.get(j);
-            hideStart = region[0];
-            hideEnd = region[1];
-
-            if (hideStart < start)
-            {
-              continue;
-            }
-
-            blockStart = Math.min(blockStart, hideEnd + 1);
-            blockEnd = Math.min(blockEnd, hideStart);
-
-            if (blockStart > blockEnd)
-            {
-              break;
-            }
-
-            visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
-
-            blockStart = hideEnd + 1;
-            blockEnd = end;
-          }
-
-          if (end > blockStart)
-          {
-            visibleSeq.append(seqs[i].getSequence(blockStart, end));
-          }
+      int[] reveal = null;
 
-          selections[i] = visibleSeq.toString();
-        }
-      }
-      else
+      if (!hiddenColumns.isEmpty())
       {
-        for (int i = 0; i < iSize; i++)
+        // look for a region ending just before adjres
+        int regionindex = cursor.findRegionForColumn(adjres - 1, false)
+                .getRegionIndex();
+        if (regionindex < hiddenColumns.size()
+                && hiddenColumns.get(regionindex)[1] == adjres - 1)
+        {
+          reveal = hiddenColumns.get(regionindex);
+        }
+        // check if the region ends just after adjres
+        else if (regionindex < hiddenColumns.size()
+                && hiddenColumns.get(regionindex)[0] == adjres + 1)
         {
-          selections[i] = seqs[i].getSequenceAsString(start, end);
+          reveal = hiddenColumns.get(regionindex);
         }
       }
+      return reveal;
 
-      return selections;
     } finally
     {
       LOCK.readLock().unlock();
@@ -901,92 +1001,14 @@ public class HiddenColumns
   }
 
   /**
-   * Locate the first and last position visible for this sequence. if seq isn't
-   * visible then return the position of the left and right of the hidden
-   * boundary region, and the corresponding alignment column indices for the
-   * extent of the sequence
-   * 
-   * @param seq
-   * @return int[] { visible start, visible end, first seqpos, last seqpos,
-   *         alignment index for seq start, alignment index for seq end }
+   * Return an iterator over the hidden regions
    */
-  public int[] locateVisibleBoundsOfSequence(SequenceI seq)
+  public Iterator<int[]> iterator()
   {
     try
     {
       LOCK.readLock().lock();
-      int fpos = seq.getStart();
-      int lpos = seq.getEnd();
-      int start = 0;
-
-      if (hiddenColumns == null || hiddenColumns.size() == 0)
-      {
-        int ifpos = seq.findIndex(fpos) - 1;
-        int ilpos = seq.findIndex(lpos) - 1;
-        return new int[] { ifpos, ilpos, fpos, lpos, ifpos, ilpos };
-      }
-
-      // Simply walk along the sequence whilst watching for hidden column
-      // boundaries
-      List<int[]> regions = getHiddenRegions();
-      int spos = fpos;
-      int lastvispos = -1;
-      int rcount = 0;
-      int hideStart = seq.getLength();
-      int hideEnd = -1;
-      int visPrev = 0;
-      int visNext = 0;
-      int firstP = -1;
-      int lastP = -1;
-      boolean foundStart = false;
-      for (int p = 0, pLen = seq.getLength(); spos <= seq.getEnd()
-              && p < pLen; p++)
-      {
-        if (!Comparison.isGap(seq.getCharAt(p)))
-        {
-          // keep track of first/last column
-          // containing sequence data regardless of visibility
-          if (firstP == -1)
-          {
-            firstP = p;
-          }
-          lastP = p;
-          // update hidden region start/end
-          while (hideEnd < p && rcount < regions.size())
-          {
-            int[] region = regions.get(rcount++);
-            visPrev = visNext;
-            visNext += region[0] - visPrev;
-            hideStart = region[0];
-            hideEnd = region[1];
-          }
-          if (hideEnd < p)
-          {
-            hideStart = seq.getLength();
-          }
-          // update visible boundary for sequence
-          if (p < hideStart)
-          {
-            if (!foundStart)
-            {
-              fpos = spos;
-              start = p;
-              foundStart = true;
-            }
-            lastvispos = p;
-            lpos = spos;
-          }
-          // look for next sequence position
-          spos++;
-        }
-      }
-      if (foundStart)
-      {
-        return new int[] { findColumnPosition(start),
-            findColumnPosition(lastvispos), fpos, lpos, firstP, lastP };
-      }
-      // otherwise, sequence was completely hidden
-      return new int[] { visPrev, visNext, 0, 0, firstP, lastP };
+      return new RangeIterator(hiddenColumns);
     } finally
     {
       LOCK.readLock().unlock();
@@ -994,120 +1016,54 @@ public class HiddenColumns
   }
 
   /**
-   * delete any columns in alignmentAnnotation that are hidden (including
-   * sequence associated annotation).
+   * Return a bounded iterator over the hidden regions
    * 
-   * @param alignmentAnnotation
+   * @param start
+   *          position to start from (inclusive, absolute column position)
+   * @param end
+   *          position to end at (inclusive, absolute column position)
+   * @return
    */
-  public void makeVisibleAnnotation(AlignmentAnnotation alignmentAnnotation)
+  public Iterator<int[]> getBoundedIterator(int start, int end)
   {
-    makeVisibleAnnotation(-1, -1, alignmentAnnotation);
+    try
+    {
+      LOCK.readLock().lock();
+      return new RangeIterator(start, end, hiddenColumns);
+    } finally
+    {
+      LOCK.readLock().unlock();
+    }
   }
 
   /**
-   * delete any columns in alignmentAnnotation that are hidden (including
-   * sequence associated annotation).
+   * Return a bounded iterator over the *visible* start positions of hidden
+   * regions
    * 
    * @param start
-   *          remove any annotation to the right of this column
+   *          position to start from (inclusive, visible column position)
    * @param end
-   *          remove any annotation to the left of this column
-   * @param alignmentAnnotation
-   *          the annotation to operate on
+   *          position to end at (inclusive, visible column position)
    */
-  public void makeVisibleAnnotation(int start, int end,
-          AlignmentAnnotation alignmentAnnotation)
+  public Iterator<Integer> getStartRegionIterator(int start, int end)
   {
     try
     {
       LOCK.readLock().lock();
-      if (alignmentAnnotation.annotations == null)
-      {
-        return;
-      }
-      if (start == end && end == -1)
-      {
-        start = 0;
-        end = alignmentAnnotation.annotations.length;
-      }
-      if (hiddenColumns != null && hiddenColumns.size() > 0)
-      {
-        // then mangle the alignmentAnnotation annotation array
-        Vector<Annotation[]> annels = new Vector<>();
-        Annotation[] els = null;
-        List<int[]> regions = getHiddenRegions();
-        int blockStart = start;
-        int blockEnd = end;
-        int[] region;
-        int hideStart;
-        int hideEnd;
-        int w = 0;
-
-        for (int j = 0; j < regions.size(); j++)
-        {
-          region = regions.get(j);
-          hideStart = region[0];
-          hideEnd = region[1];
-
-          if (hideStart < start)
-          {
-            continue;
-          }
-
-          blockStart = Math.min(blockStart, hideEnd + 1);
-          blockEnd = Math.min(blockEnd, hideStart);
-
-          if (blockStart > blockEnd)
-          {
-            break;
-          }
-
-          annels.addElement(els = new Annotation[blockEnd - blockStart]);
-          System.arraycopy(alignmentAnnotation.annotations, blockStart, els,
-                  0, els.length);
-          w += els.length;
-          blockStart = hideEnd + 1;
-          blockEnd = end;
-        }
 
-        if (end > blockStart)
-        {
-          annels.addElement(els = new Annotation[end - blockStart + 1]);
-          if ((els.length
-                  + blockStart) <= alignmentAnnotation.annotations.length)
-          {
-            // copy just the visible segment of the annotation row
-            System.arraycopy(alignmentAnnotation.annotations, blockStart,
-                    els, 0, els.length);
-          }
-          else
-          {
-            // copy to the end of the annotation row
-            System.arraycopy(alignmentAnnotation.annotations, blockStart,
-                    els, 0,
-                    (alignmentAnnotation.annotations.length - blockStart));
-          }
-          w += els.length;
-        }
-        if (w == 0)
-        {
-          return;
-        }
+      // get absolute position of column in alignment
+      int absoluteStart = visibleToAbsoluteColumn(start);
 
-        alignmentAnnotation.annotations = new Annotation[w];
-        w = 0;
+      // Get cursor position and supply it to the iterator:
+      // Since we want visible region start, we look for a cursor for the
+      // (absoluteStart-1), then if absoluteStart is the start of a visible
+      // region we'll get the cursor pointing to the region before, which is
+      // what we want
+      HiddenCursorPosition pos = cursor
+              .findRegionForColumn(absoluteStart - 1, false);
 
-        for (Annotation[] chnk : annels)
-        {
-          System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w,
-                  chnk.length);
-          w += chnk.length;
-        }
-      }
-      else
-      {
-        alignmentAnnotation.restrict(start, end);
-      }
+      return new StartRegionIterator(pos, start, end,
+              hiddenColumns);
     } finally
     {
       LOCK.readLock().unlock();
@@ -1115,15 +1071,21 @@ public class HiddenColumns
   }
 
   /**
+   * Return an iterator over visible *columns* (not regions) between the given
+   * start and end boundaries
    * 
-   * @return true if there are columns hidden
+   * @param start
+   *          first column (inclusive)
+   * @param end
+   *          last column (inclusive)
    */
-  public boolean hasHiddenColumns()
+  public Iterator<Integer> getVisibleColsIterator(int start, int end)
   {
     try
     {
       LOCK.readLock().lock();
-      return hiddenColumns != null && hiddenColumns.size() > 0;
+      return new RangeElementsIterator(
+              new VisibleContigsIterator(start, end + 1, hiddenColumns));
     } finally
     {
       LOCK.readLock().unlock();
@@ -1131,577 +1093,36 @@ public class HiddenColumns
   }
 
   /**
+   * return an iterator over visible segments between the given start and end
+   * boundaries
    * 
-   * @return true if there are more than one set of columns hidden
+   * @param start
+   *          first column, inclusive from 0
+   * @param end
+   *          last column - not inclusive
+   * @param useVisibleCoords
+   *          if true, start and end are visible column positions, not absolute
+   *          positions*
    */
-  public boolean hasManyHiddenColumns()
+  public VisibleContigsIterator getVisContigsIterator(int start,
+          int end,
+          boolean useVisibleCoords)
   {
+    int adjstart = start;
+    int adjend = end;
+    if (useVisibleCoords)
+    {
+      adjstart = visibleToAbsoluteColumn(start);
+      adjend = visibleToAbsoluteColumn(end);
+    }
+
     try
     {
       LOCK.readLock().lock();
-      return hiddenColumns != null && hiddenColumns.size() > 1;
+      return new VisibleContigsIterator(adjstart, adjend, hiddenColumns);
     } finally
     {
       LOCK.readLock().unlock();
     }
   }
-
-  /**
-   * mark the columns corresponding to gap characters as hidden in the column
-   * selection
-   * 
-   * @param sr
-   */
-  public void hideInsertionsFor(SequenceI sr)
-  {
-    try
-    {
-      LOCK.writeLock().lock();
-      List<int[]> inserts = sr.getInsertions();
-      for (int[] r : inserts)
-      {
-        hideColumns(r[0], r[1]);
-      }
-    } finally
-    {
-      LOCK.writeLock().unlock();
-    }
-  }
-
-  /**
-   * Unhides, and adds to the selection list, all hidden columns
-   */
-  public void revealAllHiddenColumns(ColumnSelection sel)
-  {
-    try
-    {
-      LOCK.writeLock().lock();
-      if (hiddenColumns != null)
-      {
-        for (int i = 0; i < hiddenColumns.size(); i++)
-        {
-          int[] region = hiddenColumns.get(i);
-          for (int j = region[0]; j < region[1] + 1; j++)
-          {
-            sel.addElement(j);
-          }
-        }
-      }
-
-      hiddenColumns = null;
-    } finally
-    {
-      LOCK.writeLock().unlock();
-    }
-  }
-
-  /**
-   * Reveals, and marks as selected, the hidden column range with the given
-   * start column
-   * 
-   * @param start
-   */
-  public void revealHiddenColumns(int start, ColumnSelection sel)
-  {
-    try
-    {
-      LOCK.writeLock().lock();
-      for (int i = 0; i < hiddenColumns.size(); i++)
-      {
-        int[] region = hiddenColumns.get(i);
-        if (start == region[0])
-        {
-          for (int j = region[0]; j < region[1] + 1; j++)
-          {
-            sel.addElement(j);
-          }
-
-          hiddenColumns.remove(region);
-          break;
-        }
-      }
-      if (hiddenColumns.size() == 0)
-      {
-        hiddenColumns = null;
-      }
-    } finally
-    {
-      LOCK.writeLock().unlock();
-    }
-  }
-
-  /**
-   * removes intersection of position,length ranges in deletions from the
-   * start,end regions marked in intervals.
-   * 
-   * @param shifts
-   * @param intervals
-   * @return
-   */
-  private boolean pruneIntervalList(final List<int[]> shifts,
-          ArrayList<int[]> intervals)
-  {
-    boolean pruned = false;
-    int i = 0;
-    int j = intervals.size() - 1;
-    int s = 0;
-    int t = shifts.size() - 1;
-    int[] hr = intervals.get(i);
-    int[] sr = shifts.get(s);
-    while (i <= j && s <= t)
-    {
-      boolean trailinghn = hr[1] >= sr[0];
-      if (!trailinghn)
-      {
-        if (i < j)
-        {
-          hr = intervals.get(++i);
-        }
-        else
-        {
-          i++;
-        }
-        continue;
-      }
-      int endshift = sr[0] + sr[1]; // deletion ranges - -ve means an insert
-      if (endshift < hr[0] || endshift < sr[0])
-      { // leadinghc disjoint or not a deletion
-        if (s < t)
-        {
-          sr = shifts.get(++s);
-        }
-        else
-        {
-          s++;
-        }
-        continue;
-      }
-      boolean leadinghn = hr[0] >= sr[0];
-      boolean leadinghc = hr[0] < endshift;
-      boolean trailinghc = hr[1] < endshift;
-      if (leadinghn)
-      {
-        if (trailinghc)
-        { // deleted hidden region.
-          intervals.remove(i);
-          pruned = true;
-          j--;
-          if (i <= j)
-          {
-            hr = intervals.get(i);
-          }
-          continue;
-        }
-        if (leadinghc)
-        {
-          hr[0] = endshift; // clip c terminal region
-          leadinghn = !leadinghn;
-          pruned = true;
-        }
-      }
-      if (!leadinghn)
-      {
-        if (trailinghc)
-        {
-          if (trailinghn)
-          {
-            hr[1] = sr[0] - 1;
-            pruned = true;
-          }
-        }
-        else
-        {
-          // sr contained in hr
-          if (s < t)
-          {
-            sr = shifts.get(++s);
-          }
-          else
-          {
-            s++;
-          }
-          continue;
-        }
-      }
-    }
-    return pruned; // true if any interval was removed or modified by
-    // operations.
-  }
-
-  /**
-   * remove any hiddenColumns or selected columns and shift remaining based on a
-   * series of position, range deletions.
-   * 
-   * @param deletions
-   */
-  public void pruneDeletions(List<int[]> shifts)
-  {
-    try
-    {
-      LOCK.writeLock().lock();
-      // delete any intervals intersecting.
-      if (hiddenColumns != null)
-      {
-        pruneIntervalList(shifts, hiddenColumns);
-        if (hiddenColumns != null && hiddenColumns.size() == 0)
-        {
-          hiddenColumns = null;
-        }
-      }
-    } finally
-    {
-      LOCK.writeLock().unlock();
-    }
-  }
-
-  /**
-   * Add gaps into the sequences aligned to profileseq under the given
-   * AlignmentView
-   * 
-   * @param profileseq
-   * @param al
-   *          - alignment to have gaps inserted into it
-   * @param input
-   *          - alignment view where sequence corresponding to profileseq is
-   *          first entry
-   * @return new HiddenColumns for new alignment view, with insertions into
-   *         profileseq marked as hidden.
-   */
-  public static HiddenColumns propagateInsertions(SequenceI profileseq,
-          AlignmentI al, AlignmentView input)
-  {
-    int profsqpos = 0;
-
-    char gc = al.getGapCharacter();
-    Object[] alandhidden = input.getAlignmentAndHiddenColumns(gc);
-    HiddenColumns nview = (HiddenColumns) alandhidden[1];
-    SequenceI origseq = ((SequenceI[]) alandhidden[0])[profsqpos];
-    nview.propagateInsertions(profileseq, al, origseq);
-    return nview;
-  }
-
-  /**
-   * 
-   * @param profileseq
-   *          - sequence in al which corresponds to origseq
-   * @param al
-   *          - alignment which is to have gaps inserted into it
-   * @param origseq
-   *          - sequence corresponding to profileseq which defines gap map for
-   *          modifying al
-   */
-  private void propagateInsertions(SequenceI profileseq, AlignmentI al,
-          SequenceI origseq)
-  {
-    char gc = al.getGapCharacter();
-    // recover mapping between sequence's non-gap positions and positions
-    // mapping to view.
-    pruneDeletions(ShiftList.parseMap(origseq.gapMap()));
-    int[] viscontigs = getVisibleContigs(0, profileseq.getLength());
-    int spos = 0;
-    int offset = 0;
-
-    // add profile to visible contigs
-    for (int v = 0; v < viscontigs.length; v += 2)
-    {
-      if (viscontigs[v] > spos)
-      {
-        StringBuffer sb = new StringBuffer();
-        for (int s = 0, ns = viscontigs[v] - spos; s < ns; s++)
-        {
-          sb.append(gc);
-        }
-        for (int s = 0, ns = al.getHeight(); s < ns; s++)
-        {
-          SequenceI sqobj = al.getSequenceAt(s);
-          if (sqobj != profileseq)
-          {
-            String sq = al.getSequenceAt(s).getSequenceAsString();
-            if (sq.length() <= spos + offset)
-            {
-              // pad sequence
-              int diff = spos + offset - sq.length() - 1;
-              if (diff > 0)
-              {
-                // pad gaps
-                sq = sq + sb;
-                while ((diff = spos + offset - sq.length() - 1) > 0)
-                {
-                  // sq = sq
-                  // + ((diff >= sb.length()) ? sb.toString() : sb
-                  // .substring(0, diff));
-                  if (diff >= sb.length())
-                  {
-                    sq += sb.toString();
-                  }
-                  else
-                  {
-                    char[] buf = new char[diff];
-                    sb.getChars(0, diff, buf, 0);
-                    sq += buf.toString();
-                  }
-                }
-              }
-              sq += sb.toString();
-            }
-            else
-            {
-              al.getSequenceAt(s).setSequence(sq.substring(0, spos + offset)
-                      + sb.toString() + sq.substring(spos + offset));
-            }
-          }
-        }
-        // offset+=sb.length();
-      }
-      spos = viscontigs[v + 1] + 1;
-    }
-    if ((offset + spos) < profileseq.getLength())
-    {
-      // pad the final region with gaps.
-      StringBuffer sb = new StringBuffer();
-      for (int s = 0, ns = profileseq.getLength() - spos
-              - offset; s < ns; s++)
-      {
-        sb.append(gc);
-      }
-      for (int s = 0, ns = al.getHeight(); s < ns; s++)
-      {
-        SequenceI sqobj = al.getSequenceAt(s);
-        if (sqobj == profileseq)
-        {
-          continue;
-        }
-        String sq = sqobj.getSequenceAsString();
-        // pad sequence
-        int diff = origseq.getLength() - sq.length();
-        while (diff > 0)
-        {
-          // sq = sq
-          // + ((diff >= sb.length()) ? sb.toString() : sb
-          // .substring(0, diff));
-          if (diff >= sb.length())
-          {
-            sq += sb.toString();
-          }
-          else
-          {
-            char[] buf = new char[diff];
-            sb.getChars(0, diff, buf, 0);
-            sq += buf.toString();
-          }
-          diff = origseq.getLength() - sq.length();
-        }
-      }
-    }
-  }
-
-  /**
-   * remove any hiddenColumns or selected columns and shift remaining based on a
-   * series of position, range deletions.
-   * 
-   * @param deletions
-   */
-  private void pruneDeletions(ShiftList deletions)
-  {
-    if (deletions != null)
-    {
-      final List<int[]> shifts = deletions.getShifts();
-      if (shifts != null && shifts.size() > 0)
-      {
-        pruneDeletions(shifts);
-
-        // and shift the rest.
-        this.compensateForEdits(deletions);
-      }
-    }
-  }
-
-  /**
-   * Adjust hidden column boundaries based on a series of column additions or
-   * deletions in visible regions.
-   * 
-   * @param shiftrecord
-   * @return
-   */
-  private ShiftList compensateForEdits(ShiftList shiftrecord)
-  {
-    if (shiftrecord != null)
-    {
-      final List<int[]> shifts = shiftrecord.getShifts();
-      if (shifts != null && shifts.size() > 0)
-      {
-        int shifted = 0;
-        for (int i = 0, j = shifts.size(); i < j; i++)
-        {
-          int[] sh = shifts.get(i);
-          compensateForDelEdits(shifted + sh[0], sh[1]);
-          shifted -= sh[1];
-        }
-      }
-      return shiftrecord.getInverse();
-    }
-    return null;
-  }
-
-  /**
-   * Returns a hashCode built from hidden column ranges
-   */
-  @Override
-  public int hashCode()
-  {
-    try
-    {
-      LOCK.readLock().lock();
-      int hashCode = 1;
-      if (hiddenColumns != null)
-      {
-        for (int[] hidden : hiddenColumns)
-        {
-          hashCode = 31 * hashCode + hidden[0];
-          hashCode = 31 * hashCode + hidden[1];
-        }
-      }
-      return hashCode;
-    } finally
-    {
-      LOCK.readLock().unlock();
-    }
-  }
-
-  /**
-   * Hide columns corresponding to the marked bits
-   * 
-   * @param inserts
-   *          - columns map to bits starting from zero
-   */
-  public void hideMarkedBits(BitSet inserts)
-  {
-    try
-    {
-      LOCK.writeLock().lock();
-      for (int firstSet = inserts
-              .nextSetBit(0), lastSet = 0; firstSet >= 0; firstSet = inserts
-                      .nextSetBit(lastSet))
-      {
-        lastSet = inserts.nextClearBit(firstSet);
-        hideColumns(firstSet, lastSet - 1);
-      }
-    } finally
-    {
-      LOCK.writeLock().unlock();
-    }
-  }
-
-  /**
-   * 
-   * @param inserts
-   *          BitSet where hidden columns will be marked
-   */
-  public void markHiddenRegions(BitSet inserts)
-  {
-    try
-    {
-      LOCK.readLock().lock();
-      if (hiddenColumns == null)
-      {
-        return;
-      }
-      for (int[] range : hiddenColumns)
-      {
-        inserts.set(range[0], range[1] + 1);
-      }
-    } finally
-    {
-      LOCK.readLock().unlock();
-    }
-  }
-
-  /**
-   * Calculate the visible start and end index of an alignment.
-   * 
-   * @param width
-   *          full alignment width
-   * @return integer array where: int[0] = startIndex, and int[1] = endIndex
-   */
-  public int[] getVisibleStartAndEndIndex(int width)
-  {
-    try
-    {
-      LOCK.readLock().lock();
-      int[] alignmentStartEnd = new int[] { 0, width - 1 };
-      int startPos = alignmentStartEnd[0];
-      int endPos = alignmentStartEnd[1];
-
-      int[] lowestRange = new int[] { -1, -1 };
-      int[] higestRange = new int[] { -1, -1 };
-
-      if (hiddenColumns == null)
-      {
-        return new int[] { startPos, endPos };
-      }
-
-      for (int[] hiddenCol : hiddenColumns)
-      {
-        lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
-        higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
-      }
-
-      if (lowestRange[0] == -1 && lowestRange[1] == -1)
-      {
-        startPos = alignmentStartEnd[0];
-      }
-      else
-      {
-        startPos = lowestRange[1] + 1;
-      }
-
-      if (higestRange[0] == -1 && higestRange[1] == -1)
-      {
-        endPos = alignmentStartEnd[1];
-      }
-      else
-      {
-        endPos = higestRange[0] - 1;
-      }
-      return new int[] { startPos, endPos };
-    } finally
-    {
-      LOCK.readLock().unlock();
-    }
-
-  }
-
-  /**
-   * Finds the hidden region (if any) which starts or ends at res
-   * 
-   * @param res
-   *          visible residue position, unadjusted for hidden columns
-   * @return region as [start,end] or null if no matching region is found
-   */
-  public int[] getRegionWithEdgeAtRes(int res)
-  {
-    try
-    {
-      LOCK.readLock().lock();
-      int adjres = adjustForHiddenColumns(res);
-
-      int[] reveal = null;
-      if (hiddenColumns != null)
-      {
-        for (int[] region : hiddenColumns)
-        {
-          if (adjres + 1 == region[0] || adjres - 1 == region[1])
-          {
-            reveal = region;
-            break;
-          }
-        }
-      }
-      return reveal;
-    } finally
-    {
-      LOCK.readLock().unlock();
-    }
-  }
-
 }
diff --git a/src/jalview/datamodel/HiddenColumnsCursor.java b/src/jalview/datamodel/HiddenColumnsCursor.java
new file mode 100644
index 0000000..2e9d798
--- /dev/null
+++ b/src/jalview/datamodel/HiddenColumnsCursor.java
@@ -0,0 +1,213 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.datamodel;
+
+import java.util.ArrayList;
+import java.util.List;
+
+public class HiddenColumnsCursor
+{
+  // absolute position of first hidden column
+  private int firstColumn;
+
+  private List<int[]> hiddenColumns = new ArrayList<>();
+
+  private HiddenCursorPosition cursorPos = new HiddenCursorPosition(0, 0);
+
+  protected HiddenColumnsCursor()
+  {
+
+  }
+
+  protected HiddenColumnsCursor(List<int[]> hiddenCols)
+  {
+    resetCursor(hiddenCols, 0, 0);
+  }
+
+  protected HiddenColumnsCursor(List<int[]> hiddenCols, int index,
+          int hiddencount)
+  {
+    resetCursor(hiddenCols, index, hiddencount);
+  }
+
+  /**
+   * Reset the cursor with a new hidden columns collection, where we know in
+   * advance the index and hidden columns count of a particular location.
+   * 
+   * @param hiddenCols
+   *          new hidden columns collection
+   * @param index
+   *          cursor index to reset to
+   * @param hiddencount
+   *          hidden columns count to reset to
+   */
+  private void resetCursor(List<int[]> hiddenCols, int index,
+          int hiddencount)
+  {
+    hiddenColumns = hiddenCols;
+    if (!hiddenCols.isEmpty())
+    {
+      firstColumn = hiddenColumns.get(0)[0];
+      cursorPos = new HiddenCursorPosition(index,
+              hiddencount);
+    }
+  }
+
+  /**
+   * Get the cursor pointing to the hidden region that column is within (if
+   * column is hidden) or which is to the right of column (if column is
+   * visible). If no hidden columns are to the right, returns a cursor pointing
+   * to an imaginary hidden region beyond the end of the hidden columns
+   * collection (this ensures the count of previous hidden columns is correct).
+   * If hidden columns is empty returns null.
+   * 
+   * @param column
+   *          index of column in visible or absolute coordinates
+   * @param useVisible
+   *          true if column is in visible coordinates, false if absolute
+   * @return cursor pointing to hidden region containing the column (if hidden)
+   *         or to the right of the column (if visible)
+   */
+  protected HiddenCursorPosition findRegionForColumn(int column,
+          boolean useVisible)
+  {
+    if (hiddenColumns.isEmpty())
+    {
+      return null;
+    }
+
+    // used to add in hiddenColumns offset when working with visible columns
+    int offset = (useVisible ? 1 : 0);
+
+    HiddenCursorPosition pos = cursorPos;
+    int index = pos.getRegionIndex();
+    int hiddenCount = pos.getHiddenSoFar();
+
+    if (column < firstColumn)
+    {
+      pos = new HiddenCursorPosition(0, 0);
+    }
+
+    // column is after current region
+    else if ((index < hiddenColumns.size())
+            && (hiddenColumns.get(index)[0] <= column
+                    + offset * hiddenCount))
+    {
+      // iterate from where we are now, if we're lucky we'll be close by
+      // (but still better than iterating from 0)
+      // stop when we find the region *before* column
+      // i.e. the next region starts after column or if not, ends after column
+      pos = searchForward(pos, column, useVisible);
+    }
+
+    // column is before current region
+    else
+    {
+      pos = searchBackward(pos, column, useVisible);
+    }
+    cursorPos = pos;
+    return pos;
+  }
+
+  /**
+   * Search forwards through the hidden columns collection to find the hidden
+   * region immediately before a column
+   * 
+   * @param pos
+   *          current position
+   * @param column
+   *          column to locate
+   * @param useVisible
+   *          whether using visible or absolute coordinates
+   * @return position of region before column
+   */
+  private HiddenCursorPosition searchForward(HiddenCursorPosition pos,
+          int column, boolean useVisible)
+  {
+    HiddenCursorPosition p = pos;
+    if (useVisible)
+    {
+      while ((p.getRegionIndex() < hiddenColumns.size())
+              && hiddenColumns.get(p.getRegionIndex())[0] <= column
+                      + p.getHiddenSoFar())
+      {
+        p = stepForward(p);
+      }
+    }
+    else
+    {
+      while ((p.getRegionIndex() < hiddenColumns.size())
+              && hiddenColumns.get(p.getRegionIndex())[1] < column)
+      {
+        p = stepForward(p);
+      }
+    }
+    return p;
+  }
+
+  /**
+   * Move to the next (rightwards) hidden region after a given cursor position
+   * 
+   * @param p
+   *          current position of cursor
+   * @return new position of cursor at next region
+   */
+  private HiddenCursorPosition stepForward(HiddenCursorPosition p)
+  {
+    int[] region = hiddenColumns.get(p.getRegionIndex());
+
+    // increment the index, and add this region's hidden columns to the hidden
+    // column count
+    return new HiddenCursorPosition(p.getRegionIndex() + 1,
+            p.getHiddenSoFar() + region[1] - region[0] + 1);
+  }
+
+  /**
+   * Search backwards through the hidden columns collection to find the hidden
+   * region immediately before (left of) a given column
+   * 
+   * @param pos
+   *          current position
+   * @param column
+   *          column to locate
+   * @param useVisible
+   *          whether using visible or absolute coordinates
+   * @return position of region immediately to left of column
+   */
+  private HiddenCursorPosition searchBackward(HiddenCursorPosition p,
+          int column, boolean useVisible)
+  {
+    int i = p.getRegionIndex();
+    int h = p.getHiddenSoFar();
+
+    // used to add in hiddenColumns offset when working with visible columns
+    int offset = (useVisible ? 1 : 0);
+
+    while ((i > 0) && (hiddenColumns.get(i - 1)[1] >= column + offset * h))
+    {
+      i--;
+      int[] region = hiddenColumns.get(i);
+      h -= region[1] - region[0] + 1;
+    }
+    return new HiddenCursorPosition(i, h);
+  }
+
+}
diff --git a/src/jalview/datamodel/HiddenCursorPosition.java b/src/jalview/datamodel/HiddenCursorPosition.java
new file mode 100644
index 0000000..160ed71
--- /dev/null
+++ b/src/jalview/datamodel/HiddenCursorPosition.java
@@ -0,0 +1,26 @@
+package jalview.datamodel;
+
+public final class HiddenCursorPosition
+{
+  // index of last visited region
+  private final int regionIndex;
+
+  // number of hidden columns before last visited region
+  private final int hiddenSoFar;
+
+  public HiddenCursorPosition(int index, int hiddencount)
+  {
+    regionIndex = index;
+    hiddenSoFar = hiddencount;
+  }
+
+  public int getRegionIndex()
+  {
+    return regionIndex;
+  }
+
+  public int getHiddenSoFar()
+  {
+    return hiddenSoFar;
+  }
+}
diff --git a/src/jalview/datamodel/HiddenMarkovModel.java b/src/jalview/datamodel/HiddenMarkovModel.java
new file mode 100644
index 0000000..a4270cd
--- /dev/null
+++ b/src/jalview/datamodel/HiddenMarkovModel.java
@@ -0,0 +1,612 @@
+package jalview.datamodel;
+
+import jalview.io.HMMFile;
+import jalview.schemes.ResidueProperties;
+import jalview.util.Comparison;
+import jalview.util.MapList;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+/**
+ * Data structure which stores a hidden Markov model
+ * 
+ * @author TZVanaalten
+ * 
+ */
+public class HiddenMarkovModel
+{
+  private static final char GAP_DASH = '-';
+
+  public final static String YES = "yes";
+
+  public final static String NO = "no";
+
+  public static final int MATCHTOMATCH = 0;
+
+  public static final int MATCHTOINSERT = 1;
+
+  public static final int MATCHTODELETE = 2;
+
+  public static final int INSERTTOMATCH = 3;
+
+  public static final int INSERTTOINSERT = 4;
+
+  public static final int DELETETOMATCH = 5;
+
+  public static final int DELETETODELETE = 6;
+
+  private static final double LOG2 = Math.log(2);
+
+  /*
+   * properties read from HMM file header lines
+   */
+  private Map<String, String> fileProperties = new HashMap<>();
+
+  private String fileHeader;
+  
+  /*
+   * the symbols used in this model e.g. "ACGT"
+   */
+  private String alphabet;
+
+  /*
+   * symbol lookup index into the alphabet for 'A' to 'Z'
+   */
+  private int[] symbolIndexLookup = new int['Z' - 'A' + 1];
+
+  /*
+   * Nodes in the model. The begin node is at index 0, and contains 
+   * average emission probabilities for each symbol.
+   */
+  private List<HMMNode> nodes = new ArrayList<>();
+
+  /*
+   * the aligned HMM consensus sequence extracted from the HMM profile
+   */
+  private SequenceI hmmSeq;
+
+  /*
+   * mapping from HMM nodes to residues of the hmm consensus sequence
+   */
+  private Mapping mapToHmmConsensus;
+
+  /**
+   * Constructor
+   */
+  public HiddenMarkovModel()
+  {
+  }
+
+  /**
+   * Copy constructor
+   * 
+   * @param hmm
+   */
+  public HiddenMarkovModel(HiddenMarkovModel hmm)
+  {
+    super();
+    this.fileProperties = new HashMap<>(hmm.fileProperties);
+    this.alphabet = hmm.alphabet;
+    this.nodes = new ArrayList<>(hmm.nodes);
+    this.symbolIndexLookup = hmm.symbolIndexLookup;
+    this.fileHeader = new String(hmm.fileHeader);
+  }
+
+  /**
+   * Returns the information content at a specified column, calculated as the
+   * sum (over possible symbols) of the log ratio
+   * 
+   * <pre>
+   *  log(emission probability / background probability) / log(2)
+   * </pre>
+   * 
+   * @param column
+   *          column position (base 0)
+   * @return
+   */
+  public float getInformationContent(int column)
+  {
+    float informationContent = 0f;
+
+    for (char symbol : getSymbols().toCharArray())
+    {
+      float freq = ResidueProperties.backgroundFrequencies
+              .get(getAlphabetType()).get(symbol);
+      float prob = (float) getMatchEmissionProbability(column, symbol);
+      informationContent += prob * Math.log(prob / freq);
+    }
+
+    informationContent = informationContent / (float) LOG2;
+
+    return informationContent;
+  }
+
+  /**
+   * Gets the file header of the .hmm file this model came from
+   * 
+   * @return
+   */
+  public String getFileHeader()
+  {
+    return fileHeader;
+  }
+
+  /**
+   * Sets the file header of this model.
+   * 
+   * @param header
+   */
+  public void setFileHeader(String header)
+  {
+    fileHeader = header;
+  }
+
+  /**
+   * Returns the symbols used in this hidden Markov model
+   * 
+   * @return
+   */
+  public String getSymbols()
+  {
+    return alphabet;
+  }
+  
+  /**
+   * Gets the node in the hidden Markov model at the specified position.
+   * 
+   * @param nodeIndex
+   *          The index of the node requested. Node 0 optionally contains the
+   *          average match emission probabilities across the entire model, and
+   *          always contains the insert emission probabilities and state
+   *          transition probabilities for the begin node. Node 1 contains the
+   *          first node in the HMM that can correspond to a column in the
+   *          alignment.
+   * @return
+   */
+  public HMMNode getNode(int nodeIndex)
+  {
+    return nodes.get(nodeIndex);
+  }
+
+  /**
+   * Returns the name of the sequence alignment on which the HMM is based.
+   * 
+   * @return
+   */
+  public String getName()
+  {
+    return fileProperties.get(HMMFile.NAME);
+  }
+  
+  /**
+   * Answers the string value of the property (parsed from an HMM file) for the
+   * given key, or null if the property is not present
+   * 
+   * @param key
+   * @return
+   */
+  public String getProperty(String key)
+  {
+    return fileProperties.get(key);
+  }
+
+  /**
+   * Answers true if the property with the given key is present with a value of
+   * "yes" (not case-sensitive), else false
+   * 
+   * @param key
+   * @return
+   */
+  public boolean getBooleanProperty(String key)
+  {
+    return YES.equalsIgnoreCase(fileProperties.get(key));
+  }
+
+  /**
+   * Returns the length of the hidden Markov model. The value returned is the
+   * LENG property if specified, else the number of nodes, excluding the begin
+   * node (which should be the same thing).
+   * 
+   * @return
+   */
+  public int getLength()
+  {
+    if (fileProperties.get(HMMFile.LENGTH) == null)
+    {
+      return nodes.size() - 1; // not counting BEGIN node
+    }
+    return Integer.parseInt(fileProperties.get(HMMFile.LENGTH));
+  }
+
+  /**
+   * Returns the value of mandatory property "ALPH" - "amino", "DNA", "RNA" are
+   * the options. Other alphabets may be added.
+   * 
+   * @return
+   */
+  public String getAlphabetType()
+  {
+    return fileProperties.get(HMMFile.ALPHABET);
+  }
+
+  /**
+   * Sets the model alphabet to the symbols in the given string (ignoring any
+   * whitespace), and returns the number of symbols
+   * 
+   * @param symbols
+   */
+  public int setAlphabet(String symbols)
+  {
+    String trimmed = symbols.toUpperCase().replaceAll("\\s", "");
+    int count = trimmed.length();
+    alphabet = trimmed;
+    symbolIndexLookup = new int['Z' - 'A' + 1];
+    Arrays.fill(symbolIndexLookup, -1);
+    int ignored = 0;
+
+    /*
+     * save the symbols in order, and a quick lookup of symbol position
+     */
+    for (short i = 0; i < count; i++)
+    {
+      char symbol = trimmed.charAt(i);
+      if (symbol >= 'A' && symbol <= 'Z'
+              && symbolIndexLookup[symbol - 'A'] == -1)
+      {
+        symbolIndexLookup[symbol - 'A'] = i;
+      }
+      else
+      {
+        System.err
+                .println(
+                        "Unexpected or duplicated character in HMM ALPHabet: "
+                                + symbol);
+        ignored++;
+      }
+    }
+    return count - ignored;
+  }
+
+  /**
+   * Answers the node of the model corresponding to an aligned column position
+   * (0...), or null if there is no such node
+   * 
+   * @param column
+   * @return
+   */
+  HMMNode getNodeForColumn(int column)
+  {
+    /*
+     * if the hmm consensus is gapped at the column,
+     * there is no corresponding node
+     */
+    if (Comparison.isGap(hmmSeq.getCharAt(column)))
+    {
+      return null;
+    }
+
+    /*
+     * find the node (if any) that is mapped to the
+     * consensus sequence residue position at the column
+     */
+    int seqPos = hmmSeq.findPosition(column);
+    int[] nodeNo = mapToHmmConsensus.getMap().locateInFrom(seqPos, seqPos);
+    if (nodeNo != null)
+    {
+      return getNode(nodeNo[0]);
+    }
+    return null;
+  }
+
+  /**
+   * Gets the match emission probability for a given symbol at a column in the
+   * alignment.
+   * 
+   * @param alignColumn
+   *          The index of the alignment column, starting at index 0. Index 0
+   *          usually corresponds to index 1 in the HMM.
+   * @param symbol
+   *          The symbol for which the desired probability is being requested.
+   * @return
+   * 
+   */
+  public double getMatchEmissionProbability(int alignColumn, char symbol)
+  {
+    HMMNode node = getNodeForColumn(alignColumn);
+    int symbolIndex = getSymbolIndex(symbol);
+    if (node != null && symbolIndex != -1)
+    {
+      return node.getMatchEmission(symbolIndex);
+    }
+    return 0D;
+  }
+
+  /**
+   * Gets the insert emission probability for a given symbol at a column in the
+   * alignment.
+   * 
+   * @param alignColumn
+   *          The index of the alignment column, starting at index 0. Index 0
+   *          usually corresponds to index 1 in the HMM.
+   * @param symbol
+   *          The symbol for which the desired probability is being requested.
+   * @return
+   * 
+   */
+  public double getInsertEmissionProbability(int alignColumn, char symbol)
+  {
+    HMMNode node = getNodeForColumn(alignColumn);
+    int symbolIndex = getSymbolIndex(symbol);
+    if (node != null && symbolIndex != -1)
+    {
+      return node.getInsertEmission(symbolIndex);
+    }
+    return 0D;
+  }
+  
+  /**
+   * Gets the state transition probability for a given symbol at a column in the
+   * alignment.
+   * 
+   * @param alignColumn
+   *          The index of the alignment column, starting at index 0. Index 0
+   *          usually corresponds to index 1 in the HMM.
+   * @param symbol
+   *          The symbol for which the desired probability is being requested.
+   * @return
+   * 
+   */
+  public double getStateTransitionProbability(int alignColumn,
+          int transition)
+  {
+    HMMNode node = getNodeForColumn(alignColumn);
+    if (node != null)
+    {
+      return node.getStateTransition(transition);
+    }
+    return 0D;
+  }
+  
+  /**
+   * Returns the sequence position linked to the node at the given index. This
+   * corresponds to an aligned column position (counting from 1).
+   * 
+   * @param nodeIndex
+   *          The index of the node, starting from index 1. Index 0 is the begin
+   *          node, which does not correspond to a column in the alignment.
+   * @return
+   */
+  public int getNodeMapPosition(int nodeIndex)
+  {
+    return nodes.get(nodeIndex).getResidueNumber();
+  }
+  
+  /**
+   * Returns the consensus residue at the specified node.
+   * 
+   * @param nodeIndex
+   *          The index of the specified node.
+   * @return
+   */
+  public char getConsensusResidue(int nodeIndex)
+  {
+   char value = nodes.get(nodeIndex).getConsensusResidue();
+   return value;
+  }
+  
+  /**
+   * Returns the reference annotation at the specified node.
+   * 
+   * @param nodeIndex
+   *          The index of the specified node.
+   * @return
+   */
+  public char getReferenceAnnotation(int nodeIndex)
+  {
+   char value = nodes.get(nodeIndex).getReferenceAnnotation();
+   return value;
+  }
+  
+  /**
+   * Returns the mask value at the specified node.
+   * 
+   * @param nodeIndex
+   *          The index of the specified node.
+   * @return
+   */
+  public char getMaskedValue(int nodeIndex)
+  {
+   char value = nodes.get(nodeIndex).getMaskValue();
+   return value;
+  }
+  
+  /**
+   * Returns the consensus structure at the specified node.
+   * 
+   * @param nodeIndex
+   *          The index of the specified node.
+   * @return
+   */
+  public char getConsensusStructure(int nodeIndex)
+  {
+   char value = nodes.get(nodeIndex).getConsensusStructure();
+   return value;
+  }
+  
+  /**
+   * Sets a property read from an HMM file
+   * 
+   * @param key
+   * @param value
+   */
+  public void setProperty(String key, String value)
+  {
+    fileProperties.put(key, value);
+  }
+
+  /**
+   * Temporary implementation, should not be used.
+   * 
+   * @return
+   */
+  public String getViterbi()
+  {
+    String value;
+    value = fileProperties.get(HMMFile.VITERBI);
+    return value;
+  }
+
+  /**
+   * Temporary implementation, should not be used.
+   * 
+   * @return
+   */
+  public String getMSV()
+  {
+    String value;
+    value = fileProperties.get(HMMFile.MSV);
+    return value;
+  }
+
+  /**
+   * Temporary implementation, should not be used.
+   * 
+   * @return
+   */
+  public String getForward()
+  {
+    String value;
+    value = fileProperties.get(HMMFile.FORWARD);
+    return value;
+  }
+
+  /**
+   * Constructs the consensus sequence based on the most probable symbol at each
+   * position. Gap characters are inserted for discontinuities in the node map
+   * numbering (if provided), else an ungapped sequence is generated.
+   * <p>
+   * A mapping between the HMM nodes and residue positions of the sequence is
+   * also built and saved.
+   * 
+   * @return
+   */
+  void buildConsensusSequence()
+  {
+    List<int[]> toResidues = new ArrayList<>();
+
+    /*
+     * if the HMM provided a map to sequence, use those start/end values,
+     * else just treat it as for a contiguous sequence numbered from 1
+     */
+    boolean hasMap = getBooleanProperty(HMMFile.MAP);
+    int start = hasMap ? getNode(1).getResidueNumber() : 1;
+    int endResNo = hasMap ? getNode(nodes.size() - 1).getResidueNumber()
+            : (start + getLength() - 1);
+    char[] sequence = new char[endResNo - start + 1];
+
+    int lastResNo = start - 1;
+    int seqOffset = 0;
+    int gapCount = 0;
+
+    for (int nodeNo = 1; nodeNo < nodes.size(); nodeNo++)
+    {
+      HMMNode node = nodes.get(nodeNo);
+      final int resNo = hasMap ? node.getResidueNumber() : lastResNo + 1;
+
+      /*
+       * insert gaps if map numbering is not continuous
+       */
+      while (resNo > lastResNo + 1)
+      {
+        sequence[seqOffset++] = '-';
+        lastResNo++;
+        gapCount++;
+      }
+      char consensusResidue = node.getConsensusResidue();
+      if (GAP_DASH == consensusResidue)
+      {
+        /*
+         * no residue annotation in HMM - scan for the symbol
+         * with the highest match emission probability
+         */
+        int symbolIndex = node.getMaxMatchEmissionIndex();
+        consensusResidue = alphabet.charAt(symbolIndex);
+        if (node.getMatchEmission(symbolIndex) < 0.5D)
+        {
+          // follow convention of lower case if match emission prob < 0.5
+          consensusResidue = Character.toLowerCase(consensusResidue);
+        }
+      }
+      sequence[seqOffset++] = consensusResidue;
+      lastResNo = resNo;
+    }
+
+    Sequence seq = new Sequence(getName(), sequence, start,
+            lastResNo - gapCount);
+    seq.createDatasetSequence();
+    seq.setHMM(this);
+    seq.setIsHMMConsensusSequence(true);
+
+    this.hmmSeq = seq;
+
+    /*
+     * construct and store Mapping of nodes to residues
+     * note as constructed this is just an identity mapping, 
+     * but it allows for greater flexibility in future
+     */
+    List<int[]> fromNodes = new ArrayList<>();
+    fromNodes.add(new int[] { 1, getLength() });
+    toResidues.add(new int[] { seq.getStart(), seq.getEnd() });
+    MapList mapList = new MapList(fromNodes, toResidues, 1, 1);
+    mapToHmmConsensus = new Mapping(seq.getDatasetSequence(), mapList);
+  }
+
+
+  /**
+   * Answers the aligned consensus sequence for the profile. Note this will
+   * return null if called before <code>setNodes</code> has been called.
+   * 
+   * @return
+   */
+  public SequenceI getConsensusSequence()
+  {
+    return hmmSeq;
+  }
+
+  /**
+   * Answers the index position (0...) of the given symbol, or -1 if not a valid
+   * symbol for this HMM
+   * 
+   * @param symbol
+   * @return
+   */
+  private int getSymbolIndex(char symbol)
+  {
+    /*
+     * symbolIndexLookup holds the index for 'A' to 'Z'
+     */
+    char c = Character.toUpperCase(symbol);
+    if ('A' <= c && c <= 'Z')
+    {
+      return symbolIndexLookup[c - 'A'];
+    }
+    return -1;
+  }
+
+  /**
+   * Sets the nodes of this HMM, and also extracts the HMM consensus sequence
+   * and a mapping between node numbers and sequence positions
+   * 
+   * @param nodeList
+   */
+  public void setNodes(List<HMMNode> nodeList)
+  {
+    nodes = nodeList;
+    buildConsensusSequence();
+  }
+}
+
diff --git a/src/jalview/datamodel/RangeElementsIterator.java b/src/jalview/datamodel/RangeElementsIterator.java
new file mode 100644
index 0000000..85272f2
--- /dev/null
+++ b/src/jalview/datamodel/RangeElementsIterator.java
@@ -0,0 +1,88 @@
+package jalview.datamodel;
+
+import java.util.Iterator;
+import java.util.NoSuchElementException;
+
+/**
+ * Iterator over each element in a set of ranges i.e. if ranges is {[3,6],
+ * [12,15]} it will iterate over {3,4,5,6,12,13,14,15}. Uses a local copy of the
+ * set of ranges.
+ * 
+ * @author kmourao
+ *
+ */
+public class RangeElementsIterator implements Iterator<Integer>
+{
+  private int last;
+
+  private int current;
+
+  private int next;
+
+  private Iterator<int[]> rangeIterator;
+
+  private int[] nextRange = null;
+
+  RangeElementsIterator(Iterator<int[]> it)
+  {
+    rangeIterator = it;
+    if (rangeIterator.hasNext())
+    {
+      nextRange = rangeIterator.next();
+      next = nextRange[0];
+      last = nextRange[1];
+    }
+  }
+
+  @Override
+  public boolean hasNext()
+  {
+    return rangeIterator.hasNext() || next <= last;
+  }
+
+  @Override
+  public Integer next()
+  {
+    if (!hasNext())
+    {
+      throw new NoSuchElementException();
+    }
+
+    current = next;
+
+    // recalculate next
+    next++;
+
+    // if there are more ranges need to check if next is in a range
+    checkNextRange();
+    return current;
+  }
+
+  /**
+   * Check how next position relates to next range, and update next position if
+   * necessary
+   */
+  private void checkNextRange()
+  {
+    if (nextRange != null && next > nextRange[1])
+    {
+      if (rangeIterator.hasNext())
+      {
+        nextRange = rangeIterator.next();
+        next = nextRange[0];
+        last = nextRange[1];
+      }
+      else
+      {
+        nextRange = null;
+      }
+
+    }
+  }
+
+  @Override
+  public void remove()
+  {
+    throw new UnsupportedOperationException();
+  }
+}
diff --git a/src/jalview/datamodel/RangeIterator.java b/src/jalview/datamodel/RangeIterator.java
new file mode 100644
index 0000000..7a69ac6
--- /dev/null
+++ b/src/jalview/datamodel/RangeIterator.java
@@ -0,0 +1,114 @@
+package jalview.datamodel;
+
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
+/**
+ * An iterator which iterates over a list of ranges. Works with a copy of the
+ * collection of ranges.
+ */
+public class RangeIterator implements Iterator<int[]>
+{
+  // current index in rangeList
+  private int currentPosition = 0;
+
+  // current range in rangeList
+  private int[] currentRange;
+
+  // local copy or reference to rangeList
+  private List<int[]> localRanges;
+
+  /**
+   * Unbounded constructor
+   * 
+   * @param rangeList
+   *          list of ranges to iterate over
+   */
+  RangeIterator(List<int[]> rangeList)
+  {
+    if (!rangeList.isEmpty())
+    {
+      int last = rangeList.get(rangeList.size() - 1)[1];
+      init(0, last, rangeList);
+    }
+    else
+    {
+      init(0, 0, rangeList);
+    }
+  }
+
+  /**
+   * Construct an iterator over rangeList bounded at [lowerBound,upperBound]
+   * 
+   * @param lowerBound
+   *          lower bound to iterate from
+   * @param upperBound
+   *          upper bound to iterate to
+   * @param rangeList
+   *          list of ranges to iterate over
+   */
+  RangeIterator(int lowerBound, int upperBound,
+          List<int[]> rangeList)
+  {
+    init(lowerBound, upperBound, rangeList);
+  }
+
+  /**
+   * Construct an iterator over rangeList bounded at [lowerBound,upperBound]
+   * 
+   * @param lowerBound
+   *          lower bound to iterate from
+   * @param upperBound
+   *          upper bound to iterate to
+   */
+  private void init(int lowerBound, int upperBound,
+          List<int[]> rangeList)
+  {
+    int start = lowerBound;
+    int end = upperBound;
+
+    if (rangeList != null)
+    {
+      localRanges = new ArrayList<>();
+
+      // iterate until a range overlaps with [start,end]
+      int i = 0;
+      while ((i < rangeList.size()) && (rangeList.get(i)[1] < start))
+      {
+        i++;
+      }
+
+      // iterate from start to end, adding each range. Positions are
+      // absolute, and all ranges which *overlap* [start,end] are added.
+      while (i < rangeList.size() && (rangeList.get(i)[0] <= end))
+      {
+        int[] rh = rangeList.get(i);
+        int[] cp = new int[2];
+        System.arraycopy(rh, 0, cp, 0, rh.length);
+        localRanges.add(cp);
+        i++;
+      }
+    }
+  }
+
+  @Override
+  public boolean hasNext()
+  {
+    return (localRanges != null) && (currentPosition < localRanges.size());
+  }
+
+  @Override
+  public int[] next()
+  {
+    currentRange = localRanges.get(currentPosition);
+    currentPosition++;
+    return currentRange;
+  }
+
+  @Override
+  public void remove()
+  {
+    localRanges.remove(--currentPosition);
+  }
+}
diff --git a/src/jalview/datamodel/ResidueCount.java b/src/jalview/datamodel/ResidueCount.java
index 74eb887..047b7e7 100644
--- a/src/jalview/datamodel/ResidueCount.java
+++ b/src/jalview/datamodel/ResidueCount.java
@@ -25,6 +25,8 @@ import jalview.util.Format;
 import jalview.util.QuickSort;
 import jalview.util.SparseCount;
 
+import java.util.List;
+
 /**
  * A class to count occurrences of residues in a profile, optimised for speed
  * and memory footprint.
@@ -148,6 +150,24 @@ public class ResidueCount
   }
 
   /**
+   * A constructor that counts frequency of all symbols (including gaps) in the
+   * sequences (not case-sensitive)
+   * 
+   * @param sequences
+   */
+  public ResidueCount(List<SequenceI> sequences)
+  {
+    this();
+    for (SequenceI seq : sequences)
+    {
+      for (int i = 0; i < seq.getLength(); i++)
+      {
+        add(seq.getCharAt(i));
+      }
+    }
+  }
+
+  /**
    * Increments the count for the given character. The supplied character may be
    * upper or lower case but counts are for the upper case only. Gap characters
    * (space, ., -) are all counted together.
@@ -640,4 +660,19 @@ public class ResidueCount
     sb.append("]");
     return sb.toString();
   }
+
+  /**
+   * Answers the total count for all symbols (excluding gaps)
+   * 
+   * @return
+   */
+  public int getTotalResidueCount()
+  {
+    int total = 0;
+    for (char symbol : this.getSymbolCounts().symbols)
+    {
+      total += getCount(symbol);
+    }
+    return total;
+  }
 }
diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 441d8d0..755abbb 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -28,12 +28,14 @@ import jalview.util.Comparison;
 import jalview.util.DBRefUtils;
 import jalview.util.MapList;
 import jalview.util.StringUtils;
+import jalview.workers.InformationThread;
 
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.BitSet;
 import java.util.Collections;
 import java.util.Enumeration;
+import java.util.Iterator;
 import java.util.List;
 import java.util.ListIterator;
 import java.util.Vector;
@@ -61,6 +63,10 @@ public class Sequence extends ASequence implements SequenceI
 
   int end;
 
+  HiddenMarkovModel hmm;
+
+  boolean isHMMConsensusSequence = false;
+
   Vector<PDBEntry> pdbIds;
 
   String vamsasId;
@@ -337,6 +343,15 @@ public class Sequence extends ASequence implements SequenceI
         this.addPDBId(new PDBEntry(pdb));
       }
     }
+    if (seq.isHMMConsensusSequence())
+    {
+      this.isHMMConsensusSequence = true;
+    }
+    if (seq.getHMM() != null)
+    {
+      this.hmm = new HiddenMarkovModel(seq.getHMM());
+    }
+
   }
 
   @Override
@@ -408,7 +423,7 @@ public class Sequence extends ASequence implements SequenceI
   {
     if (pdbIds == null)
     {
-      pdbIds = new Vector<PDBEntry>();
+      pdbIds = new Vector<>();
       pdbIds.add(entry);
       return true;
     }
@@ -444,7 +459,7 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public Vector<PDBEntry> getAllPDBEntries()
   {
-    return pdbIds == null ? new Vector<PDBEntry>() : pdbIds;
+    return pdbIds == null ? new Vector<>() : pdbIds;
   }
 
   /**
@@ -1128,6 +1143,27 @@ public class Sequence extends ASequence implements SequenceI
     return map;
   }
 
+  /**
+   * Build a bitset corresponding to sequence gaps
+   * 
+   * @return a BitSet where set values correspond to gaps in the sequence
+   */
+  @Override
+  public BitSet gapBitset()
+  {
+    BitSet gaps = new BitSet(sequence.length);
+    int j = 0;
+    while (j < sequence.length)
+    {
+      if (jalview.util.Comparison.isGap(sequence[j]))
+      {
+        gaps.set(j);
+      }
+      j++;
+    }
+    return gaps;
+  }
+
   @Override
   public int[] findPositionMap()
   {
@@ -1151,7 +1187,7 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public List<int[]> getInsertions()
   {
-    ArrayList<int[]> map = new ArrayList<int[]>();
+    ArrayList<int[]> map = new ArrayList<>();
     int lastj = -1, j = 0;
     int pos = start;
     int seqlen = sequence.length;
@@ -1462,7 +1498,7 @@ public class Sequence extends ASequence implements SequenceI
   {
     if (this.annotation == null)
     {
-      this.annotation = new Vector<AlignmentAnnotation>();
+      this.annotation = new Vector<>();
     }
     if (!this.annotation.contains(annotation))
     {
@@ -1629,7 +1665,7 @@ public class Sequence extends ASequence implements SequenceI
       return null;
     }
 
-    Vector<AlignmentAnnotation> subset = new Vector<AlignmentAnnotation>();
+    Vector<AlignmentAnnotation> subset = new Vector<>();
     Enumeration<AlignmentAnnotation> e = annotation.elements();
     while (e.hasMoreElements())
     {
@@ -1763,12 +1799,13 @@ public class Sequence extends ASequence implements SequenceI
   public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
           String label)
   {
-    List<AlignmentAnnotation> result = new ArrayList<AlignmentAnnotation>();
+    List<AlignmentAnnotation> result = new ArrayList<>();
     if (this.annotation != null)
     {
       for (AlignmentAnnotation ann : annotation)
       {
-        if (ann.calcId != null && ann.calcId.equals(calcId)
+        String id = ann.getCalcId();
+        if (id != null && id.equals(calcId)
                 && ann.label != null && ann.label.equals(label))
         {
           result.add(ann);
@@ -1819,7 +1856,7 @@ public class Sequence extends ASequence implements SequenceI
     }
     synchronized (dbrefs)
     {
-      List<DBRefEntry> primaries = new ArrayList<DBRefEntry>();
+      List<DBRefEntry> primaries = new ArrayList<>();
       DBRefEntry[] tmp = new DBRefEntry[1];
       for (DBRefEntry ref : dbrefs)
       {
@@ -1866,6 +1903,46 @@ public class Sequence extends ASequence implements SequenceI
     }
   }
 
+  @Override
+  public HiddenMarkovModel getHMM()
+  {
+    return hmm;
+  }
+
+  @Override
+  public void setHMM(HiddenMarkovModel hmm)
+  {
+    this.hmm = hmm;
+  }
+
+  @Override
+  public boolean isHMMConsensusSequence()
+  {
+    return isHMMConsensusSequence;
+  }
+
+  @Override
+  public void setIsHMMConsensusSequence(boolean value)
+  {
+    this.isHMMConsensusSequence = value;
+  }
+
+  @Override
+  public boolean hasHMMAnnotation()
+  {
+    if (this.annotation == null) {
+      return false;
+    }
+    for (AlignmentAnnotation ann : annotation)
+    {
+      if (InformationThread.HMM_CALC_ID.equals(ann.getCalcId()))
+      {
+        return true;
+      }
+    }
+    return false;
+  }
+
   /**
    * {@inheritDoc}
    */
@@ -1961,4 +2038,73 @@ public class Sequence extends ASequence implements SequenceI
 
     return count;
   }
+
+  @Override
+  public String getSequenceStringFromIterator(Iterator<int[]> it)
+  {
+    StringBuilder newSequence = new StringBuilder();
+    while (it.hasNext())
+    {
+      int[] block = it.next();
+      if (it.hasNext())
+      {
+        newSequence.append(getSequence(block[0], block[1] + 1));
+      }
+      else
+      {
+        newSequence.append(getSequence(block[0], block[1]));
+      }
+    }
+
+    return newSequence.toString();
+  }
+
+  @Override
+  public int firstResidueOutsideIterator(Iterator<int[]> regions)
+  {
+    int start = 0;
+
+    if (!regions.hasNext())
+    {
+      return findIndex(getStart()) - 1;
+    }
+
+    // Simply walk along the sequence whilst watching for region
+    // boundaries
+    int hideStart = getLength();
+    int hideEnd = -1;
+    boolean foundStart = false;
+
+    // step through the non-gapped positions of the sequence
+    for (int i = getStart(); i <= getEnd() && (!foundStart); i++)
+    {
+      // get alignment position of this residue in the sequence
+      int p = findIndex(i) - 1;
+
+      // update region start/end
+      while (hideEnd < p && regions.hasNext())
+      {
+        int[] region = regions.next();
+        hideStart = region[0];
+        hideEnd = region[1];
+      }
+      if (hideEnd < p)
+      {
+        hideStart = getLength();
+      }
+      // update boundary for sequence
+      if (p < hideStart)
+      {
+        start = p;
+        foundStart = true;
+      }
+    }
+
+    if (foundStart)
+    {
+      return start;
+    }
+    // otherwise, sequence was completely hidden
+    return 0;
+  }
 }
diff --git a/src/jalview/datamodel/SequenceCollectionI.java b/src/jalview/datamodel/SequenceCollectionI.java
index f681f11..ee4b844 100644
--- a/src/jalview/datamodel/SequenceCollectionI.java
+++ b/src/jalview/datamodel/SequenceCollectionI.java
@@ -70,4 +70,16 @@ public interface SequenceCollectionI
    * @return
    */
   boolean isNucleotide();
+
+  /**
+   * Returns the HMM consensus sequence (if any) for the collection, or null
+   * 
+   * @return
+   */
+  SequenceI getHmmConsensus();
+
+  /**
+   * Sets the HMM consensus sequence for the collection
+   */
+  void setHmmConsensus(SequenceI hmmSeq);
 }
diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 6b797d7..aebcbb3 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -25,6 +25,8 @@ import jalview.analysis.Conservation;
 import jalview.renderer.ResidueShader;
 import jalview.renderer.ResidueShaderI;
 import jalview.schemes.ColourSchemeI;
+import jalview.util.MessageManager;
+import jalview.workers.InformationThread;
 
 import java.awt.Color;
 import java.beans.PropertyChangeListener;
@@ -43,116 +45,120 @@ import java.util.Map;
 public class SequenceGroup implements AnnotatedCollectionI
 {
   // TODO ideally this event notification functionality should be separated into
-  // a
-  // subclass of ViewportProperties similarly to ViewportRanges. Done here as
-  // quick fix for JAL-2665
+  // a subclass of ViewportProperties similarly to ViewportRanges.
+  // Done here as a quick fix for JAL-2665
   public static final String SEQ_GROUP_CHANGED = "Sequence group changed";
 
-  protected PropertyChangeSupport changeSupport = new PropertyChangeSupport(
-          this);
+  private String groupName;
 
-  public void addPropertyChangeListener(PropertyChangeListener listener)
-  {
-    changeSupport.addPropertyChangeListener(listener);
-  }
+  private String description;
 
-  public void removePropertyChangeListener(PropertyChangeListener listener)
-  {
-    changeSupport.removePropertyChangeListener(listener);
-  }
-  // end of event notification functionality initialisation
+  private AnnotatedCollectionI context;
 
-  String groupName;
+  private Conservation conservationData;
 
-  String description;
+  private ProfilesI consensusProfiles;
 
-  Conservation conserve;
+  private ProfilesI hmmProfiles;
 
-  boolean displayBoxes = true;
+  private boolean displayBoxes = true;
 
-  boolean displayText = true;
+  private boolean displayText = true;
 
-  boolean colourText = false;
+  private boolean colourText = false;
 
-  /**
-   * True if the group is defined as a group on the alignment, false if it is
-   * just a selection.
+  /*
+   * true if the group is defined as a group on the alignment, false if it is
+   * just a selection
    */
-  boolean isDefined = false;
+  private boolean isDefined;
 
-  /**
+  /*
    * after Olivier's non-conserved only character display
    */
-  boolean showNonconserved = false;
+  private boolean showNonconserved;
 
-  /**
-   * group members
+  /*
+   * sequences in the group
    */
   private List<SequenceI> sequences = new ArrayList<>();
 
-  /**
+  /*
    * representative sequence for this group (if any)
    */
-  private SequenceI seqrep = null;
+  private SequenceI seqrep;
+
+  /*
+   * HMM consensus sequence for group (if any)
+   */
+  private SequenceI hmmConsensus;
 
-  int width = -1;
+  private int width = -1;
 
-  /**
-   * Colourscheme applied to group if any
+  /*
+   * colour scheme applied to group if any
    */
   public ResidueShaderI cs;
 
   // start column (base 0)
-  int startRes = 0;
+  private int startRes;
 
   // end column (base 0)
-  int endRes = 0;
+  private int endRes;
 
   public Color outlineColour = Color.black;
 
-  public Color idColour = null;
+  public Color idColour;
 
-  public int thresholdTextColour = 0;
+  public int thresholdTextColour;
 
   public Color textColour = Color.black;
 
   public Color textColour2 = Color.white;
 
-  /**
-   * consensus calculation property
+  /*
+   * properties for consensus annotation
    */
   private boolean ignoreGapsInConsensus = true;
 
-  /**
-   * consensus calculation property
-   */
-  private boolean showSequenceLogo = false;
+  private boolean showSequenceLogo;
 
-  /**
-   * flag indicating if logo should be rendered normalised
-   */
   private boolean normaliseSequenceLogo;
 
+  private boolean showConsensusHistogram;
+
+  /*
+   * properties for HMM information annotation
+   */
+  private boolean hmmIgnoreBelowBackground = true;
+
+  private boolean hmmUseInfoLetterHeight;
+
+  private boolean hmmShowSequenceLogo;
+
+  private boolean hmmNormaliseSequenceLogo;
+
+  private boolean hmmShowHistogram;
+
   /*
    * visibility of rows or represented rows covered by group
    */
-  private boolean hidereps = false;
+  private boolean hidereps;
 
   /*
    * visibility of columns intersecting this group
    */
-  private boolean hidecols = false;
-
-  AlignmentAnnotation consensus = null;
+  private boolean hidecols;
 
-  AlignmentAnnotation conservation = null;
+  private AlignmentAnnotation consensus;
 
-  private boolean showConsensusHistogram;
+  private AlignmentAnnotation conservation;
 
-  private AnnotatedCollectionI context;
+  private AlignmentAnnotation hmmInformation;
 
   /**
-   * Creates a new SequenceGroup object.
+   * Constructor, assigning a generated default name of "JGroup:" with object
+   * hashcode appended
    */
   public SequenceGroup()
   {
@@ -222,6 +228,9 @@ public class SequenceGroup implements AnnotatedCollectionI
       showSequenceLogo = seqsel.showSequenceLogo;
       normaliseSequenceLogo = seqsel.normaliseSequenceLogo;
       showConsensusHistogram = seqsel.showConsensusHistogram;
+      hmmShowSequenceLogo = seqsel.hmmShowSequenceLogo;
+      hmmNormaliseSequenceLogo = seqsel.hmmNormaliseSequenceLogo;
+      hmmShowHistogram = seqsel.hmmShowHistogram;
       idColour = seqsel.idColour;
       outlineColour = seqsel.outlineColour;
       seqrep = seqsel.seqrep;
@@ -230,7 +239,9 @@ public class SequenceGroup implements AnnotatedCollectionI
       thresholdTextColour = seqsel.thresholdTextColour;
       width = seqsel.width;
       ignoreGapsInConsensus = seqsel.ignoreGapsInConsensus;
-      if (seqsel.conserve != null)
+      hmmIgnoreBelowBackground = seqsel.hmmIgnoreBelowBackground;
+      hmmUseInfoLetterHeight = seqsel.hmmUseInfoLetterHeight;
+      if (seqsel.conservationData != null)
       {
         recalcConservation(); // safer than
         // aaFrequency = (Vector) seqsel.aaFrequency.clone(); // ??
@@ -238,6 +249,19 @@ public class SequenceGroup implements AnnotatedCollectionI
     }
   }
 
+  protected PropertyChangeSupport changeSupport = new PropertyChangeSupport(
+          this);
+
+  public void addPropertyChangeListener(PropertyChangeListener listener)
+  {
+    changeSupport.addPropertyChangeListener(listener);
+  }
+
+  public void removePropertyChangeListener(PropertyChangeListener listener)
+  {
+    changeSupport.removePropertyChangeListener(listener);
+  }
+
   public boolean isShowSequenceLogo()
   {
     return showSequenceLogo;
@@ -259,6 +283,7 @@ public class SequenceGroup implements AnnotatedCollectionI
         seqs[ipos].setDescription(seq.getDescription());
         seqs[ipos].setDBRefs(seq.getDBRefs());
         seqs[ipos].setSequenceFeatures(seq.getSequenceFeatures());
+        seqs[ipos].setIsHMMConsensusSequence(seq.isHMMConsensusSequence());
         if (seq.getDatasetSequence() != null)
         {
           seqs[ipos].setDatasetSequence(seq.getDatasetSequence());
@@ -488,7 +513,7 @@ public class SequenceGroup implements AnnotatedCollectionI
    */
   public Conservation getConservation()
   {
-    return conserve;
+    return conservationData;
   }
 
   /**
@@ -499,7 +524,7 @@ public class SequenceGroup implements AnnotatedCollectionI
    */
   public void setConservation(Conservation c)
   {
-    conserve = c;
+    conservationData = c;
   }
 
   /**
@@ -560,20 +585,22 @@ public class SequenceGroup implements AnnotatedCollectionI
    */
   public boolean recalcConservation()
   {
-    return recalcConservation(false);
+    return recalcAnnotations(false);
   }
 
   /**
-   * calculate residue conservation for group - but only if necessary. returns
-   * true if the calculation resulted in a visible change to group
+   * Recalculates column consensus, conservation, and HMM annotation for the
+   * group (as applicable). Returns true if the calculation resulted in a
+   * visible change to group.
    * 
    * @param defer
    *          when set, colourschemes for this group are not refreshed after
    *          recalculation
    */
-  public boolean recalcConservation(boolean defer)
+  public boolean recalcAnnotations(boolean defer)
   {
-    if (cs == null && consensus == null && conservation == null)
+    if (cs == null && consensus == null && conservation == null
+            && hmmInformation == null)
     {
       return false;
     }
@@ -584,6 +611,16 @@ public class SequenceGroup implements AnnotatedCollectionI
     {
       ProfilesI cnsns = AAFrequency.calculate(sequences, startRes,
               endRes + 1, showSequenceLogo);
+      if (hmmInformation != null)
+      {
+        HiddenMarkovModel hmm = hmmInformation.sequenceRef.getHMM();
+
+        ProfilesI info = AAFrequency.calculateHMMProfiles(hmm,
+                (endRes + 1) - startRes, startRes, endRes + 1,
+                hmmIgnoreBelowBackground, hmmUseInfoLetterHeight);
+        _updateInformationRow(info);
+        upd = true;
+      }
       if (consensus != null)
       {
         _updateConsensusRow(cnsns, sequences.size());
@@ -656,8 +693,6 @@ public class SequenceGroup implements AnnotatedCollectionI
     c.completeAnnotations(conservation, null, startRes, endRes + 1);
   }
 
-  public ProfilesI consensusData = null;
-
   private void _updateConsensusRow(ProfilesI cnsns, long nseq)
   {
     if (consensus == null)
@@ -666,7 +701,7 @@ public class SequenceGroup implements AnnotatedCollectionI
     }
     consensus.label = "Consensus for " + getName();
     consensus.description = "Percent Identity";
-    consensusData = cnsns;
+    consensusProfiles = cnsns;
     // preserve width if already set
     int aWidth = (consensus.annotations != null)
             ? (endRes < consensus.annotations.length
@@ -684,6 +719,33 @@ public class SequenceGroup implements AnnotatedCollectionI
   }
 
   /**
+   * Recalculates the information content on the HMM annotation
+   * 
+   * @param cnsns
+   */
+  private void _updateInformationRow(ProfilesI cnsns)
+  {
+    if (hmmInformation == null)
+    {
+      createInformationAnnotation();
+    }
+    hmmInformation.description = MessageManager
+            .getString("label.information_description");
+    setHmmProfiles(cnsns);
+    // preserve width if already set
+    int aWidth = (hmmInformation.annotations != null)
+            ? (endRes < hmmInformation.annotations.length
+                    ? hmmInformation.annotations.length : endRes + 1)
+            : endRes + 1;
+    hmmInformation.annotations = null;
+    hmmInformation.annotations = new Annotation[aWidth]; // should be alignment
+                                                      // width
+    hmmInformation.setCalcId(InformationThread.HMM_CALC_ID);
+    AAFrequency.completeInformation(hmmInformation, cnsns, startRes,
+            endRes + 1);
+  }
+
+  /**
    * @param s
    *          sequence to either add or remove from group
    * @param recalc
@@ -1137,6 +1199,22 @@ public class SequenceGroup implements AnnotatedCollectionI
   }
 
   /**
+   * Creates the Hidden Markov Model annotation for this group
+   */
+  void createInformationAnnotation()
+  {
+    hmmInformation = new AlignmentAnnotation("", "", new Annotation[1], 0f,
+            6.25f, AlignmentAnnotation.BAR_GRAPH);
+    hmmInformation.hasText = true;
+    hmmInformation.autoCalculated = false;
+    hmmInformation.groupRef = this;
+    hmmInformation.label = getName();
+    hmmInformation.description = MessageManager
+            .getString("label.information_description");
+    hmmInformation.setCalcId(InformationThread.HMM_CALC_ID);
+  }
+
+  /**
    * set this alignmentAnnotation object as the one used to render consensus
    * annotation
    * 
@@ -1189,9 +1267,10 @@ public class SequenceGroup implements AnnotatedCollectionI
     {
       if (consensus.annotations[i] != null)
       {
-        if (consensus.annotations[i].description.charAt(0) == '[')
+        String desc = consensus.annotations[i].description;
+        if (desc.length() > 1 && desc.charAt(0) == '[')
         {
-          seqs.append(consensus.annotations[i].description.charAt(1));
+          seqs.append(desc.charAt(1));
         }
         else
         {
@@ -1217,11 +1296,31 @@ public class SequenceGroup implements AnnotatedCollectionI
     ignoreGapsInConsensus = state;
   }
 
-  public boolean getIgnoreGapsConsensus()
+  public boolean isIgnoreGapsConsensus()
   {
     return ignoreGapsInConsensus;
   }
 
+  public void setIgnoreBelowBackground(boolean state)
+  {
+    hmmIgnoreBelowBackground = state;
+  }
+
+  public boolean isIgnoreBelowBackground()
+  {
+    return hmmIgnoreBelowBackground;
+  }
+
+  public void setInfoLetterHeight(boolean state)
+  {
+    hmmUseInfoLetterHeight = state;
+  }
+
+  public boolean isUseInfoLetterHeight()
+  {
+    return hmmUseInfoLetterHeight;
+  }
+
   /**
    * @param showSequenceLogo
    *          indicates if a sequence logo is shown for consensus annotation
@@ -1465,4 +1564,67 @@ public class SequenceGroup implements AnnotatedCollectionI
   {
     return (startRes <= apos && endRes >= apos) && sequences.contains(seq);
   }
+
+  public boolean isShowInformationHistogram()
+  {
+    return hmmShowHistogram;
+  }
+
+  public void setShowInformationHistogram(boolean state)
+  {
+    if (hmmShowHistogram != state && hmmInformation != null)
+    {
+      this.hmmShowHistogram = state;
+      // recalcConservation(); TODO don't know what to do here next
+    }
+    this.hmmShowHistogram = state;
+  }
+
+  public boolean isShowHMMSequenceLogo()
+  {
+    return hmmShowSequenceLogo;
+  }
+
+  public void setShowHMMSequenceLogo(boolean state)
+  {
+    hmmShowSequenceLogo = state;
+  }
+
+  public boolean isNormaliseHMMSequenceLogo()
+  {
+    return hmmNormaliseSequenceLogo;
+  }
+
+  public void setNormaliseHMMSequenceLogo(boolean state)
+  {
+    hmmNormaliseSequenceLogo = state;
+  }
+
+  @Override
+  public SequenceI getHmmConsensus()
+  {
+    return hmmConsensus;
+  }
+
+  @Override
+  public void setHmmConsensus(SequenceI hmmSeq)
+  {
+    this.hmmConsensus = hmmSeq;
+  }
+
+  public ProfilesI getConsensusData()
+  {
+    return consensusProfiles;
+  }
+
+  public ProfilesI getHmmProfiles()
+  {
+    return hmmProfiles;
+  }
+
+  public void setHmmProfiles(ProfilesI hmmProfiles)
+  {
+    this.hmmProfiles = hmmProfiles;
+  }
+
 }
diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index fb723e6..5b3d782 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -24,6 +24,7 @@ import jalview.datamodel.features.SequenceFeaturesI;
 import jalview.util.MapList;
 
 import java.util.BitSet;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Vector;
 
@@ -45,6 +46,10 @@ public interface SequenceI extends ASequenceI
    */
   public void setName(String name);
 
+  public HiddenMarkovModel getHMM();
+
+  public void setHMM(HiddenMarkovModel hmm);
+
   /**
    * Get the display name
    */
@@ -224,6 +229,13 @@ public interface SequenceI extends ASequenceI
   public int[] gapMap();
 
   /**
+   * Build a bitset corresponding to sequence gaps
+   * 
+   * @return a BitSet where set values correspond to gaps in the sequence
+   */
+  public BitSet gapBitset();
+
+  /**
    * Returns an int array where indices correspond to each position in sequence
    * char array and the element value gives the result of findPosition for that
    * index in the sequence.
@@ -487,6 +499,16 @@ public interface SequenceI extends ASequenceI
    */
   public List<DBRefEntry> getPrimaryDBRefs();
 
+  boolean isHMMConsensusSequence();
+
+  void setIsHMMConsensusSequence(boolean isHMMConsensusSequence);
+
+  /**
+   * Answers true if the sequence has annotation for Hidden Markov Model
+   * information content, else false
+   */
+  boolean hasHMMAnnotation();
+
   /**
    * Returns a (possibly empty) list of sequence features that overlap the given
    * alignment column range, optionally restricted to one or more specified
@@ -524,7 +546,7 @@ public interface SequenceI extends ASequenceI
    * @param c1
    * @param c2
    */
-  public int replace(char c1, char c2);
+  int replace(char c1, char c2);
 
   /**
    * Answers the GeneLociI, or null if not known
@@ -543,4 +565,26 @@ public interface SequenceI extends ASequenceI
    */
   void setGeneLoci(String speciesId, String assemblyId,
           String chromosomeId, MapList map);
+
+
+  /**
+   * Returns the sequence string constructed from the substrings of a sequence
+   * defined by the int[] ranges provided by an iterator. E.g. the iterator
+   * could iterate over all visible regions of the alignment
+   * 
+   * @param it
+   *          the iterator to use
+   * @return a String corresponding to the sequence
+   */
+  public String getSequenceStringFromIterator(Iterator<int[]> it);
+
+  /**
+   * Locate the first position in this sequence which is not contained in an
+   * iterator region. If no such position exists, return 0
+   * 
+   * @param it
+   *          iterator over regions
+   * @return first residue not contained in regions
+   */
+  public int firstResidueOutsideIterator(Iterator<int[]> it);
 }
diff --git a/src/jalview/datamodel/StartRegionIterator.java b/src/jalview/datamodel/StartRegionIterator.java
new file mode 100644
index 0000000..bd036e4
--- /dev/null
+++ b/src/jalview/datamodel/StartRegionIterator.java
@@ -0,0 +1,123 @@
+package jalview.datamodel;
+
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
+/**
+ * An iterator which iterates over visible start positions of hidden column
+ * regions in a range.
+ */
+public class StartRegionIterator implements Iterator<Integer>
+{
+  // start position to iterate from
+  private int start;
+
+  // end position to iterate to
+  private int end;
+
+  // current index in hiddenColumns
+  private int currentPosition = 0;
+
+  // local copy or reference to hiddenColumns
+  private List<Integer> positions = null;
+
+  /**
+   * Construct an iterator over hiddenColums bounded at [lowerBound,upperBound]
+   * 
+   * @param lowerBound
+   *          lower bound to iterate from
+   * @param upperBound
+   *          upper bound to iterate to
+   * @param useCopyCols
+   *          whether to make a local copy of hiddenColumns for iteration (set
+   *          to true if calling from outwith the HiddenColumns class)
+   */
+  StartRegionIterator(int lowerBound, int upperBound,
+          List<int[]> hiddenColumns)
+  {
+    this(null, lowerBound, upperBound, hiddenColumns);
+  }
+
+  /**
+   * Construct an iterator over hiddenColums bounded at [lowerBound,upperBound]
+   * 
+   * @param pos
+   *          a hidden cursor position to start from - may be null
+   * @param lowerBound
+   *          lower bound to iterate from - will be ignored if pos != null
+   * @param upperBound
+   *          upper bound to iterate to
+   * @param hiddenColumns
+   *          the hidden columns collection to use
+   */
+  StartRegionIterator(HiddenCursorPosition pos, int lowerBound,
+          int upperBound, List<int[]> hiddenColumns)
+  {
+    start = lowerBound;
+    end = upperBound;
+
+    if (hiddenColumns != null)
+    {
+      positions = new ArrayList<>(hiddenColumns.size());
+
+      // navigate to start, keeping count of hidden columns
+      int i = 0;
+      int hiddenSoFar = 0;
+      
+      if (pos != null)
+      {
+        // use the cursor position provided
+        i = pos.getRegionIndex();
+        hiddenSoFar = pos.getHiddenSoFar();
+      }
+      else
+      {
+        // navigate to start
+        while ((i < hiddenColumns.size())
+                && (hiddenColumns.get(i)[0] < start + hiddenSoFar))
+        {
+          int[] region = hiddenColumns.get(i);
+          hiddenSoFar += region[1] - region[0] + 1;
+          i++;
+        }
+      }
+
+      // iterate from start to end, adding start positions of each
+      // hidden region. Positions are visible columns count, not absolute
+      while (i < hiddenColumns.size()
+              && (hiddenColumns.get(i)[0] <= end + hiddenSoFar))
+      {
+        int[] region = hiddenColumns.get(i);
+        positions.add(region[0] - hiddenSoFar);
+        hiddenSoFar += region[1] - region[0] + 1;
+        i++;
+      }
+    }
+    else
+    {
+      positions = new ArrayList<>();
+    }
+
+  }
+
+  @Override
+  public boolean hasNext()
+  {
+    return (currentPosition < positions.size());
+  }
+
+  /**
+   * Get next hidden region start position
+   * 
+   * @return the start position in *visible* coordinates
+   */
+  @Override
+  public Integer next()
+  {
+    int result = positions.get(currentPosition);
+    currentPosition++;
+    return result;
+  }
+}
+
diff --git a/src/jalview/datamodel/VisibleColsCollection.java b/src/jalview/datamodel/VisibleColsCollection.java
index e9437a7..4ca51b5 100644
--- a/src/jalview/datamodel/VisibleColsCollection.java
+++ b/src/jalview/datamodel/VisibleColsCollection.java
@@ -32,17 +32,17 @@ public class VisibleColsCollection implements AlignmentColsCollectionI
 
   HiddenColumns hidden;
 
-  public VisibleColsCollection(int s, int e, AlignmentI al)
+  public VisibleColsCollection(int s, int e, HiddenColumns h)
   {
     start = s;
     end = e;
-    hidden = al.getHiddenColumns();
+    hidden = h;
   }
 
   @Override
   public Iterator<Integer> iterator()
   {
-    return new VisibleColsIterator(start, end, hidden);
+    return hidden.getVisibleColsIterator(start, end);
   }
 
   @Override
diff --git a/src/jalview/datamodel/VisibleColsIterator.java b/src/jalview/datamodel/VisibleColsIterator.java
deleted file mode 100644
index 9de468d..0000000
--- a/src/jalview/datamodel/VisibleColsIterator.java
+++ /dev/null
@@ -1,130 +0,0 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- * 
- * This file is part of Jalview.
- * 
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *  
- * Jalview is distributed in the hope that it will be useful, but 
- * WITHOUT ANY WARRANTY; without even the implied warranty 
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
- * PURPOSE.  See the GNU General Public License for more details.
- * 
- * You should have received a copy of the GNU General Public License
- * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.datamodel;
-
-import java.util.Iterator;
-import java.util.List;
-import java.util.NoSuchElementException;
-
-/**
- * An iterator which iterates over all visible columns in an alignment
- * 
- * @author kmourao
- *
- */
-public class VisibleColsIterator implements Iterator<Integer>
-{
-  private int last;
-
-  private int current;
-
-  private int next;
-
-  private List<int[]> hidden;
-
-  private int lasthiddenregion;
-
-  public VisibleColsIterator(int firstcol, int lastcol,
-          HiddenColumns hiddenCols)
-  {
-    last = lastcol;
-    current = firstcol;
-    next = firstcol;
-    hidden = hiddenCols.getHiddenColumnsCopy();
-    lasthiddenregion = -1;
-
-    if (hidden != null)
-    {
-      int i = 0;
-      for (i = 0; i < hidden.size(); ++i)
-      {
-        if (current >= hidden.get(i)[0] && current <= hidden.get(i)[1])
-        {
-          // current is hidden, move to right
-          current = hidden.get(i)[1] + 1;
-          next = current;
-        }
-        if (current < hidden.get(i)[0])
-        {
-          break;
-        }
-      }
-      lasthiddenregion = i - 1;
-
-      for (i = hidden.size() - 1; i >= 0; --i)
-      {
-        if (last >= hidden.get(i)[0] && last <= hidden.get(i)[1])
-        {
-          // last is hidden, move to left
-          last = hidden.get(i)[0] - 1;
-        }
-        if (last > hidden.get(i)[1])
-        {
-          break;
-        }
-      }
-    }
-  }
-
-  @Override
-  public boolean hasNext()
-  {
-    return next <= last;
-  }
-
-  @Override
-  public Integer next()
-  {
-    if (next > last)
-    {
-      throw new NoSuchElementException();
-    }
-    current = next;
-    if ((hidden != null) && (lasthiddenregion + 1 < hidden.size()))
-    {
-      // still some more hidden regions
-      if (next + 1 < hidden.get(lasthiddenregion + 1)[0])
-      {
-        // next+1 is still before the next hidden region
-        next++;
-      }
-      else if ((next + 1 >= hidden.get(lasthiddenregion + 1)[0])
-              && (next + 1 <= hidden.get(lasthiddenregion + 1)[1]))
-      {
-        // next + 1 is in the next hidden region
-        next = hidden.get(lasthiddenregion + 1)[1] + 1;
-        lasthiddenregion++;
-      }
-    }
-    else
-    {
-      // finished with hidden regions, just increment normally
-      next++;
-    }
-    return current;
-  }
-
-  @Override
-  public void remove()
-  {
-    throw new UnsupportedOperationException();
-  }
-}
diff --git a/src/jalview/datamodel/VisibleContigsIterator.java b/src/jalview/datamodel/VisibleContigsIterator.java
new file mode 100644
index 0000000..6d3f43d
--- /dev/null
+++ b/src/jalview/datamodel/VisibleContigsIterator.java
@@ -0,0 +1,96 @@
+package jalview.datamodel;
+
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
+/**
+ * An iterator which iterates over visible regions in a range. Provides a
+ * special "endsAtHidden" indicator to allow callers to determine if the final
+ * visible column is adjacent to a hidden region.
+ */
+public class VisibleContigsIterator implements Iterator<int[]>
+{
+  private List<int[]> vcontigs = new ArrayList<>();
+
+  private int currentPosition = 0;
+
+  private boolean endsAtHidden = false;
+
+  VisibleContigsIterator(int start, int end,
+          List<int[]> hiddenColumns)
+  {
+    if (hiddenColumns != null && hiddenColumns.size() > 0)
+    {
+      int vstart = start;
+      int hideStart;
+      int hideEnd;
+
+      for (int[] region : hiddenColumns)
+      {
+        endsAtHidden = false;
+        hideStart = region[0];
+        hideEnd = region[1];
+
+        // navigate to start
+        if (hideEnd < vstart)
+        {
+          continue;
+        }
+        if (hideStart > vstart)
+        {
+          if (end - 1 > hideStart - 1)
+          {
+            int[] contig = new int[] { vstart, hideStart - 1 };
+            vcontigs.add(contig);
+            endsAtHidden = true;
+          }
+          else
+          {
+            int[] contig = new int[] { vstart, end - 1 };
+            vcontigs.add(contig);
+          }
+        }
+        vstart = hideEnd + 1;
+
+        // exit if we're past the end
+        if (vstart >= end)
+        {
+          break;
+        }
+      }
+
+      if (vstart < end)
+      {
+        int[] contig = new int[] { vstart, end - 1 };
+        vcontigs.add(contig);
+        endsAtHidden = false;
+      }
+    }
+    else
+    {
+      int[] contig = new int[] { start, end - 1 };
+      vcontigs.add(contig);
+    }
+  }
+
+  @Override
+  public boolean hasNext()
+  {
+    return (currentPosition < vcontigs.size());
+  }
+
+  @Override
+  public int[] next()
+  {
+    int[] result = vcontigs.get(currentPosition);
+    currentPosition++;
+    return result;
+  }
+
+  public boolean endsAtHidden()
+  {
+    return endsAtHidden;
+  }
+}
+
diff --git a/src/jalview/ext/ensembl/EnsemblGenomes.java b/src/jalview/ext/ensembl/EnsemblGenomes.java
index bbd1f26..9fc6a53 100644
--- a/src/jalview/ext/ensembl/EnsemblGenomes.java
+++ b/src/jalview/ext/ensembl/EnsemblGenomes.java
@@ -20,6 +20,9 @@
  */
 package jalview.ext.ensembl;
 
+import jalview.bin.Cache;
+import jalview.datamodel.DBRefSource;
+
 /**
  * A class to behave much like EnsemblGene but referencing the ensemblgenomes
  * domain and data
@@ -35,13 +38,15 @@ public class EnsemblGenomes extends EnsemblGene
    */
   public EnsemblGenomes()
   {
-    super(ENSEMBL_GENOMES_REST);
+    super();
+    setDomain(Cache.getDefault(ENSEMBL_GENOMES_BASEURL,
+            DEFAULT_ENSEMBL_GENOMES_BASEURL));
   }
 
   @Override
   public String getDbName()
   {
-    return "EnsemblGenomes";
+    return DBRefSource.ENSEMBLGENOMES;
   }
 
   @Override
@@ -56,7 +61,7 @@ public class EnsemblGenomes extends EnsemblGene
   @Override
   public String getDbSource()
   {
-    return "EnsemblGenomes";
+    return DBRefSource.ENSEMBLGENOMES;
   }
 
 }
diff --git a/src/jalview/ext/ensembl/EnsemblInfo.java b/src/jalview/ext/ensembl/EnsemblInfo.java
index de55a53..37dff51 100644
--- a/src/jalview/ext/ensembl/EnsemblInfo.java
+++ b/src/jalview/ext/ensembl/EnsemblInfo.java
@@ -101,17 +101,17 @@ public class EnsemblInfo extends EnsemblRestClient
     /*
      * for convenience, pre-fill ensembl.org as the domain for "ENSEMBL"
      */
-    divisions.put(DBRefSource.ENSEMBL.toUpperCase(), ENSEMBL_REST);
+    divisions.put(DBRefSource.ENSEMBL.toUpperCase(), ensemblDomain);
 
     BufferedReader br = null;
     try
     {
-      URL url = getDivisionsUrl(ENSEMBL_GENOMES_REST);
+      URL url = getDivisionsUrl(ensemblGenomesDomain);
       if (url != null)
       {
         br = getHttpResponse(url, null);
       }
-      parseResponse(br, ENSEMBL_GENOMES_REST);
+      parseResponse(br, ensemblGenomesDomain);
     } catch (IOException e)
     {
       // ignore
diff --git a/src/jalview/ext/ensembl/EnsemblLookup.java b/src/jalview/ext/ensembl/EnsemblLookup.java
index f6b3a47..5f353f8 100644
--- a/src/jalview/ext/ensembl/EnsemblLookup.java
+++ b/src/jalview/ext/ensembl/EnsemblLookup.java
@@ -138,7 +138,53 @@ public class EnsemblLookup extends EnsemblRestClient
    */
   public String getGeneId(String identifier)
   {
-    return parseGeneId(getResult(identifier, null));
+    return getGeneId(identifier, null);
+  }
+
+  /**
+   * Returns the gene id related to the given identifier (which may be for a
+   * gene, transcript or protein)
+   * 
+   * @param identifier
+   * @param objectType
+   * @return
+   */
+  public String getGeneId(String identifier, String objectType)
+  {
+    return parseGeneId(getResult(identifier, objectType));
+  }
+
+  /**
+   * Parses the JSON response and returns the gene identifier, or null if not
+   * found. If the returned object_type is Gene, returns the id, if Transcript
+   * returns the Parent. If it is Translation (peptide identifier), then the
+   * Parent is the transcript identifier, so we redo the search with this value.
+   * 
+   * @param br
+   * @return
+   */
+  protected String parseGeneId(JSONObject val)
+  {
+    String geneId = null;
+    String type = val.get(OBJECT_TYPE).toString();
+    if (OBJECT_TYPE_GENE.equalsIgnoreCase(type))
+    {
+      // got the gene - just returns its id
+      geneId = val.get(JSON_ID).toString();
+    }
+    else if (OBJECT_TYPE_TRANSCRIPT.equalsIgnoreCase(type))
+    {
+      // got the transcript - return its (Gene) Parent
+      geneId = val.get(PARENT).toString();
+    }
+    else if (OBJECT_TYPE_TRANSLATION.equalsIgnoreCase(type))
+    {
+      // got the protein - get its Parent, restricted to type Transcript
+      String transcriptId = val.get(PARENT).toString();
+      geneId = getGeneId(transcriptId, OBJECT_TYPE_TRANSCRIPT);
+    }
+
+    return geneId;
   }
 
   /**
@@ -180,6 +226,7 @@ public class EnsemblLookup extends EnsemblRestClient
     try
     {
       URL url = getUrl(identifier, objectType);
+
       if (url != null)
       {
         br = getHttpResponse(url, ids);
@@ -206,46 +253,6 @@ public class EnsemblLookup extends EnsemblRestClient
   }
 
   /**
-   * Parses the JSON response and returns the gene identifier, or null if not
-   * found. If the returned object_type is Gene, returns the id, if Transcript
-   * returns the Parent. If it is Translation (peptide identifier), then the
-   * Parent is the transcript identifier, so we redo the search with this value,
-   * specifying that object_type should be Transcript.
-   * 
-   * @param jsonObject
-   * @return
-   */
-  protected String parseGeneId(JSONObject json)
-  {
-    if (json == null)
-    {
-      // e.g. lookup failed with 404 not found
-      return null;
-    }
-
-    String geneId = null;
-    String type = json.get(OBJECT_TYPE).toString();
-    if (OBJECT_TYPE_GENE.equalsIgnoreCase(type))
-    {
-      // got the gene - just returns its id
-      geneId = json.get(JSON_ID).toString();
-    }
-    else if (OBJECT_TYPE_TRANSCRIPT.equalsIgnoreCase(type))
-    {
-      // got the transcript - return its (Gene) Parent
-      geneId = json.get(PARENT).toString();
-    }
-    else if (OBJECT_TYPE_TRANSLATION.equalsIgnoreCase(type))
-    {
-      // got the protein - look up its Parent, restricted to type Transcript
-      String transcriptId = json.get(PARENT).toString();
-      geneId = parseGeneId(getResult(transcriptId, OBJECT_TYPE_TRANSCRIPT));
-    }
-
-    return geneId;
-  }
-
-  /**
    * Calls the /lookup/id rest service for the given id, and if successful,
    * parses and returns the gene's chromosomal coordinates
    * 
diff --git a/src/jalview/ext/ensembl/EnsemblRestClient.java b/src/jalview/ext/ensembl/EnsemblRestClient.java
index e3d1215..9dea886 100644
--- a/src/jalview/ext/ensembl/EnsemblRestClient.java
+++ b/src/jalview/ext/ensembl/EnsemblRestClient.java
@@ -86,10 +86,10 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
   static
   {
     domainData = new HashMap<>();
-    domainData.put(ENSEMBL_REST,
-            new EnsemblData(ENSEMBL_REST, LATEST_ENSEMBL_REST_VERSION));
-    domainData.put(ENSEMBL_GENOMES_REST, new EnsemblData(
-            ENSEMBL_GENOMES_REST, LATEST_ENSEMBLGENOMES_REST_VERSION));
+    domainData.put(DEFAULT_ENSEMBL_BASEURL,
+            new EnsemblData(DEFAULT_ENSEMBL_BASEURL, LATEST_ENSEMBL_REST_VERSION));
+    domainData.put(DEFAULT_ENSEMBL_GENOMES_BASEURL, new EnsemblData(
+            DEFAULT_ENSEMBL_GENOMES_BASEURL, LATEST_ENSEMBLGENOMES_REST_VERSION));
   }
 
   protected volatile boolean inProgress = false;
@@ -99,7 +99,21 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
    */
   public EnsemblRestClient()
   {
-    this(ENSEMBL_REST);
+    super();
+
+    /*
+     * initialise domain info lazily
+     */
+    if (!domainData.containsKey(ensemblDomain))
+    {
+      domainData.put(ensemblDomain,
+              new EnsemblData(ensemblDomain, LATEST_ENSEMBL_REST_VERSION));
+    }
+    if (!domainData.containsKey(ensemblGenomesDomain))
+    {
+      domainData.put(ensemblGenomesDomain, new EnsemblData(
+              ensemblGenomesDomain, LATEST_ENSEMBLGENOMES_REST_VERSION));
+    }
   }
 
   /**
@@ -169,11 +183,12 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
   boolean checkEnsembl()
   {
     BufferedReader br = null;
+    String pingUrl = getDomain() + "/info/ping" + CONTENT_TYPE_JSON;
     try
     {
       // note this format works for both ensembl and ensemblgenomes
       // info/ping.json works for ensembl only (March 2016)
-      URL ping = new URL(getDomain() + "/info/ping" + CONTENT_TYPE_JSON);
+      URL ping = new URL(pingUrl);
 
       /*
        * expect {"ping":1} if ok
@@ -192,7 +207,7 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
     } catch (Throwable t)
     {
       System.err.println(
-              "Error connecting to " + PING_URL + ": " + t.getMessage());
+              "Error connecting to " + pingUrl + ": " + t.getMessage());
     } finally
     {
       if (br != null)
diff --git a/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java b/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
index cfb3c6d..9e3fef4 100644
--- a/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
+++ b/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
@@ -20,6 +20,7 @@
  */
 package jalview.ext.ensembl;
 
+import jalview.bin.Cache;
 import jalview.datamodel.DBRefSource;
 import jalview.ws.seqfetcher.DbSourceProxyImpl;
 
@@ -32,6 +33,16 @@ import com.stevesoft.pat.Regex;
  */
 abstract class EnsemblSequenceFetcher extends DbSourceProxyImpl
 {
+  // domain properties lookup keys:
+  protected static final String ENSEMBL_BASEURL = "ENSEMBL_BASEURL";
+
+  protected static final String ENSEMBL_GENOMES_BASEURL = "ENSEMBL_GENOMES_BASEURL";
+
+  // domain properties default values:
+  protected static final String DEFAULT_ENSEMBL_BASEURL = "https://rest.ensembl.org";
+
+  protected static final String DEFAULT_ENSEMBL_GENOMES_BASEURL = "https://rest.ensemblgenomes.org";
+
   /*
    * accepts ENSG/T/E/P with 11 digits
    * or ENSMUSP or similar for other species
@@ -41,9 +52,9 @@ abstract class EnsemblSequenceFetcher extends DbSourceProxyImpl
           "(ENS([A-Z]{3}|)[GTEP]{1}[0-9]{11}$)" + "|"
                   + "(CCDS[0-9.]{3,}$)");
 
-  protected static final String ENSEMBL_GENOMES_REST = "http://rest.ensemblgenomes.org";
+  protected final String ensemblGenomesDomain;
 
-  protected static final String ENSEMBL_REST = "http://rest.ensembl.org";
+  protected final String ensemblDomain;
 
   protected static final String OBJECT_TYPE_TRANSLATION = "Translation";
 
@@ -68,13 +79,29 @@ abstract class EnsemblSequenceFetcher extends DbSourceProxyImpl
     constrained, regulatory
   }
 
-  private String domain = ENSEMBL_REST;
+  private String domain;
+
+  /**
+   * Constructor
+   */
+  public EnsemblSequenceFetcher()
+  {
+    /*
+     * the default domain names may be overridden in .jalview_properties;
+     * this allows an easy change from http to https in future if needed
+     */
+    ensemblDomain = Cache.getDefault(ENSEMBL_BASEURL,
+            DEFAULT_ENSEMBL_BASEURL);
+    ensemblGenomesDomain = Cache.getDefault(ENSEMBL_GENOMES_BASEURL,
+            DEFAULT_ENSEMBL_GENOMES_BASEURL);
+    domain = ensemblDomain;
+  }
 
   @Override
   public String getDbSource()
   {
     // NB ensure Uniprot xrefs are canonicalised from "Ensembl" to "ENSEMBL"
-    if (ENSEMBL_GENOMES_REST.equals(getDomain()))
+    if (ensemblGenomesDomain.equals(getDomain()))
     {
       return DBRefSource.ENSEMBLGENOMES;
     }
diff --git a/src/jalview/ext/jmol/JmolCommands.java b/src/jalview/ext/jmol/JmolCommands.java
index 6bf7010..8fb0de6 100644
--- a/src/jalview/ext/jmol/JmolCommands.java
+++ b/src/jalview/ext/jmol/JmolCommands.java
@@ -77,7 +77,6 @@ public class JmolCommands
         continue;
       }
 
-      int lastPos = -1;
       for (int s = 0; s < sequence[pdbfnum].length; s++)
       {
         for (int sp, m = 0; m < mapping.length; m++)
@@ -85,6 +84,7 @@ public class JmolCommands
           if (mapping[m].getSequence() == sequence[pdbfnum][s]
                   && (sp = al.findIndex(sequence[pdbfnum][s])) > -1)
           {
+            int lastPos = StructureMapping.UNASSIGNED_VALUE;
             SequenceI asp = al.getSequenceAt(sp);
             for (int r = 0; r < asp.getLength(); r++)
             {
@@ -95,10 +95,22 @@ public class JmolCommands
               }
               int pos = mapping[m].getPDBResNum(asp.findPosition(r));
 
-              if (pos < 1 || pos == lastPos)
+              if (pos == lastPos)
               {
                 continue;
               }
+              if (pos == StructureMapping.UNASSIGNED_VALUE)
+              {
+                // terminate current colour op
+                if (command.length() > 0
+                        && command.charAt(command.length() - 1) != ';')
+                {
+                  command.append(";");
+                }
+                // reset lastPos
+                lastPos = StructureMapping.UNASSIGNED_VALUE;
+                continue;
+              }
 
               lastPos = pos;
 
@@ -128,7 +140,12 @@ public class JmolCommands
               // TODO: deal with case when buffer is too large for Jmol to parse
               // - execute command and flush
 
-              command.append(";");
+              if (command.length() > 0
+                      && command.charAt(command.length() - 1) != ';')
+              {
+                command.append(";");
+              }
+
               if (command.length() > 51200)
               {
                 // add another chunk
diff --git a/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java b/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
index 250fba0..262ed86 100644
--- a/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
+++ b/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
@@ -21,6 +21,7 @@
 
 package jalview.fts.service.uniprot;
 
+import jalview.bin.Cache;
 import jalview.fts.api.FTSData;
 import jalview.fts.api.FTSDataColumnI;
 import jalview.fts.api.FTSRestClientI;
@@ -44,9 +45,18 @@ import com.sun.jersey.api.client.config.DefaultClientConfig;
 
 public class UniProtFTSRestClient extends FTSRestClient
 {
+  private static final String DEFAULT_UNIPROT_DOMAIN = "https://www.uniprot.org";
+
   private static FTSRestClientI instance = null;
 
-  public static final String UNIPROT_SEARCH_ENDPOINT = "http://www.uniprot.org/uniprot/?";
+  public final String uniprotSearchEndpoint;
+
+  public UniProtFTSRestClient()
+  {
+    super();
+    uniprotSearchEndpoint = Cache.getDefault("UNIPROT_DOMAIN",
+            DEFAULT_UNIPROT_DOMAIN) + "/uniprot/?";
+  }
 
   @Override
   public FTSRestResponse executeRequest(FTSRestRequest uniportRestRequest)
@@ -81,7 +91,7 @@ public class UniProtFTSRestClient extends FTSRestClient
       }
 
       WebResource webResource = null;
-      webResource = client.resource(UNIPROT_SEARCH_ENDPOINT)
+      webResource = client.resource(uniprotSearchEndpoint)
               .queryParam("format", "tab")
               .queryParam("columns", wantedFields)
               .queryParam("limit", String.valueOf(responseSize))
@@ -158,7 +168,7 @@ public class UniProtFTSRestClient extends FTSRestClient
     String[] foundDataRow = uniProtTabDelimittedResponseString.split("\n");
     if (foundDataRow != null && foundDataRow.length > 0)
     {
-      result = new ArrayList<FTSData>();
+      result = new ArrayList<>();
       boolean firstRow = true;
       for (String dataRow : foundDataRow)
       {
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 4c9360e..009d946 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -54,6 +54,7 @@ import jalview.datamodel.AlignmentOrder;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.HiddenMarkovModel;
 import jalview.datamodel.HiddenSequences;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SeqCigar;
@@ -62,6 +63,12 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.gui.ColourMenuHelper.ColourChangeListener;
 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
+import jalview.hmmer.HMMAlign;
+import jalview.hmmer.HMMBuild;
+import jalview.hmmer.HMMERParamStore;
+import jalview.hmmer.HMMERPreset;
+import jalview.hmmer.HMMSearch;
+import jalview.hmmer.HmmerCommand;
 import jalview.io.AlignmentProperties;
 import jalview.io.AnnotationFile;
 import jalview.io.BioJsHTMLOutput;
@@ -88,6 +95,7 @@ import jalview.schemes.ColourSchemes;
 import jalview.schemes.ResidueColourScheme;
 import jalview.schemes.TCoffeeColourScheme;
 import jalview.util.MessageManager;
+import jalview.util.StringUtils;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.viewmodel.ViewportRanges;
 import jalview.ws.DBRefFetcher;
@@ -95,6 +103,10 @@ import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
 import jalview.ws.jws1.Discoverer;
 import jalview.ws.jws2.Jws2Discoverer;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.ParamDatastoreI;
+import jalview.ws.params.WsParamSetI;
+import jalview.ws.params.simple.Option;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
 import java.awt.BorderLayout;
@@ -124,22 +136,29 @@ import java.awt.print.PrinterJob;
 import java.beans.PropertyChangeEvent;
 import java.io.File;
 import java.io.FileWriter;
+import java.io.IOException;
 import java.io.PrintWriter;
 import java.net.URL;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Deque;
 import java.util.Enumeration;
+import java.util.HashMap;
 import java.util.Hashtable;
 import java.util.List;
+import java.util.Map;
+import java.util.Scanner;
 import java.util.Vector;
 
 import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JEditorPane;
+import javax.swing.JFileChooser;
+import javax.swing.JFrame;
 import javax.swing.JInternalFrame;
 import javax.swing.JLayeredPane;
 import javax.swing.JMenu;
 import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
 import javax.swing.JScrollPane;
 import javax.swing.SwingUtilities;
 
@@ -153,6 +172,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 {
 
+  Map<String, Float> distribution = new HashMap<>(); // temporary
+
   public static final int DEFAULT_WIDTH = 700;
 
   public static final int DEFAULT_HEIGHT = 500;
@@ -165,6 +186,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   AlignViewport viewport;
 
   public AlignViewControllerI avc;
+  /*
+   * The selected HMM for this align frame
+   */
+  SequenceI selectedHMMSequence;
 
   List<AlignmentPanel> alignPanels = new ArrayList<>();
 
@@ -178,6 +203,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   String fileName = null;
 
+
   /**
    * Creates a new AlignFrame object with specific width and height.
    * 
@@ -762,6 +788,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       ap.av.updateConservation(ap);
       ap.av.updateConsensus(ap);
       ap.av.updateStrucConsensus(ap);
+      ap.av.initInformationWorker(ap);
     }
   }
 
@@ -904,6 +931,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
     showSequenceLogo.setSelected(av.isShowSequenceLogo());
     normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
+    showInformationHistogram.setSelected(av.isShowInformationHistogram());
+    showHMMSequenceLogo.setSelected(av.isShowHMMSequenceLogo());
+    normaliseHMMSequenceLogo.setSelected(av.isNormaliseHMMSequenceLogo());
 
     ColourMenuHelper.setColourSelected(colourMenu,
             av.getGlobalColourScheme());
@@ -995,6 +1025,198 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   @Override
+  public void hmmBuild_actionPerformed(boolean withDefaults)
+  {
+    if (!alignmentIsSufficient(1))
+    {
+      return;
+    }
+    List<ArgumentI> args = new ArrayList<>();
+    if (withDefaults)
+    {
+      // todo: construct this in HMMERPreset?
+      String argName = MessageManager.getString("label.hmmbuild_for");
+      String argValue = MessageManager.getString("label.alignment");
+      args.add(
+              new Option(argName, null, false, null, argValue, null, null));
+    }
+    else
+    {
+      WsParamSetI set = new HMMERPreset();
+      ParamDatastoreI store = HMMERParamStore.forBuild();
+      WsJobParameters params = new WsJobParameters(new JFrame(), store, set,
+              args);
+      if (params.showRunDialog())
+      {
+        args = params.getJobParams();
+      }
+      else
+      {
+        return; // user cancelled
+      }
+    }
+    new Thread(new HMMBuild(this, args)).start();
+  }
+
+  @Override
+  public void hmmAlign_actionPerformed(boolean withDefaults)
+  {
+    if (!(checkForHMM() && alignmentIsSufficient(2)))
+    {
+      return;
+    }
+    List<ArgumentI> args = new ArrayList<>();
+    if (!withDefaults)
+    {
+      WsParamSetI set = new HMMERPreset();
+      ParamDatastoreI store = HMMERParamStore.forAlign();
+      WsJobParameters params = new WsJobParameters(new JFrame(), store, set,
+              args);
+      if (params.showRunDialog())
+      {
+        args = params.getJobParams();
+      }
+      else
+      {
+        return; // user cancelled
+      }
+    }
+    new Thread(new HMMAlign(this, args)).start();
+  }
+
+  @Override
+  public void hmmSearch_actionPerformed(boolean withDefaults)
+  {
+    if (!checkForHMM())
+    {
+      return;
+    }
+    List<ArgumentI> args = new ArrayList<>();
+    if (!withDefaults)
+    {
+      WsParamSetI set = new HMMERPreset();
+      ParamDatastoreI store = HMMERParamStore.forSearch();
+      WsJobParameters params = new WsJobParameters(new JFrame(), store, set,
+              args);
+      if (params.showRunDialog())
+      {
+        args = params.getJobParams();
+      }
+      else
+      {
+        return; // user cancelled
+      }
+    }
+    new Thread(new HMMSearch(this, args)).start();
+    alignPanel.repaint();
+  }
+
+  /**
+   * Checks if the frame has a selected hidden Markov model
+   * 
+   * @return
+   */
+  private boolean checkForHMM()
+  {
+    if (getSelectedHMM() == null)
+    {
+      JOptionPane.showMessageDialog(this,
+              MessageManager.getString("warn.no_selected_hmm"));
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * Checks if the alignment contains the required number of sequences.
+   * 
+   * @param required
+   * @return
+   */
+  public boolean alignmentIsSufficient(int required)
+  {
+    if (getViewport().getAlignment().getSequences().size() < required)
+    {
+      JOptionPane.showMessageDialog(this,
+              MessageManager.getString("warn.not_enough_sequences"));
+      return false;
+    }
+    return true;
+  }
+
+  @Override
+  public void addDatabase_actionPerformed() throws IOException
+  {
+    if (Cache.getProperty(Preferences.HMMSEARCH_DB_PATHS) == null)
+    {
+      Cache.setProperty(Preferences.HMMSEARCH_DBS, "");
+      Cache.setProperty(Preferences.HMMSEARCH_DB_PATHS, "");
+    }
+
+    String path = openFileChooser(false);
+    if (new File(path).exists())
+    {
+      IdentifyFile identifier = new IdentifyFile();
+      FileFormatI format = identifier.identify(path, DataSourceType.FILE);
+      if (format == FileFormat.Fasta || format == FileFormat.Stockholm
+              || format == FileFormat.Pfam)
+      {
+        String currentDbs = Cache.getProperty(Preferences.HMMSEARCH_DBS);
+        String currentDbPaths = Cache
+                .getProperty(Preferences.HMMSEARCH_DB_PATHS);
+        currentDbPaths += " " + path;
+
+        String fileName = StringUtils.getLastToken(path, File.separator);
+        Scanner scanner = new Scanner(fileName).useDelimiter(".");
+        String name = scanner.next();
+        scanner.close();
+        currentDbs += " " + path; // TODO remove path from file name
+        scanner.close();
+
+        Cache.setProperty(Preferences.HMMSEARCH_DB_PATHS, currentDbPaths);
+        Cache.setProperty(Preferences.HMMSEARCH_DBS, currentDbPaths);
+      }
+      else
+      {
+        JOptionPane.showMessageDialog(this,
+                MessageManager.getString("warn.invalid_format"));
+      }
+    }
+    else
+    {
+      JOptionPane.showMessageDialog(this,
+              MessageManager.getString("warn.not_enough_sequences"));
+    }
+  }
+
+  /**
+   * Opens a file chooser
+   * 
+   * @param forFolder
+   * @return
+   */
+  protected String openFileChooser(boolean forFolder)
+  {
+    String choice = null;
+    JFileChooser chooser = new JFileChooser();
+    if (forFolder)
+    {
+      chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
+    }
+    chooser.setDialogTitle(
+            MessageManager.getString("label.open_local_file"));
+    chooser.setToolTipText(MessageManager.getString("action.open"));
+
+    int value = chooser.showOpenDialog(this);
+
+    if (value == JFileChooser.APPROVE_OPTION)
+    {
+      choice = chooser.getSelectedFile().getPath();
+    }
+    return choice;
+  }
+
+  @Override
   public void reload_actionPerformed(ActionEvent e)
   {
     if (fileName != null)
@@ -1403,6 +1625,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   @Override
   public void associatedData_actionPerformed(ActionEvent e)
+          throws IOException, InterruptedException
   {
     // Pick the tree file
     JalviewFileChooser chooser = new JalviewFileChooser(
@@ -1828,7 +2051,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void copy_actionPerformed(ActionEvent e)
   {
-    System.gc();
     if (viewport.getSelectionGroup() == null)
     {
       return;
@@ -1864,23 +2086,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       return;
     }
 
-    ArrayList<int[]> hiddenColumns = null;
+    HiddenColumns hiddenColumns = null;
     if (viewport.hasHiddenColumns())
     {
-      hiddenColumns = new ArrayList<>();
       int hiddenOffset = viewport.getSelectionGroup().getStartRes();
       int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
-      ArrayList<int[]> hiddenRegions = viewport.getAlignment()
-              .getHiddenColumns().getHiddenColumnsCopy();
-      for (int[] region : hiddenRegions)
-      {
-        if (region[0] >= hiddenOffset && region[1] <= hiddenCutoff)
-        {
-          hiddenColumns
-                  .add(new int[]
-                  { region[0] - hiddenOffset, region[1] - hiddenOffset });
-        }
-      }
+
+      // create new HiddenColumns object with copy of hidden regions
+      // between startRes and endRes, offset by startRes
+      hiddenColumns = new HiddenColumns(
+              viewport.getAlignment().getHiddenColumns(), hiddenOffset,
+              hiddenCutoff, hiddenOffset);
     }
 
     Desktop.jalviewClipboard = new Object[] { seqs,
@@ -1895,9 +2111,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param e
    *          DOCUMENT ME!
+   * @throws InterruptedException
+   * @throws IOException
    */
   @Override
   protected void pasteNew_actionPerformed(ActionEvent e)
+          throws IOException, InterruptedException
   {
     paste(true);
   }
@@ -1907,9 +2126,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param e
    *          DOCUMENT ME!
+   * @throws InterruptedException
+   * @throws IOException
    */
   @Override
   protected void pasteThis_actionPerformed(ActionEvent e)
+          throws IOException, InterruptedException
   {
     paste(false);
   }
@@ -1919,8 +2141,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param newAlignment
    *          true to paste to a new alignment, otherwise add to this.
+   * @throws InterruptedException
+   * @throws IOException
    */
-  void paste(boolean newAlignment)
+  void paste(boolean newAlignment) throws IOException, InterruptedException
   {
     boolean externalPaste = true;
     try
@@ -2209,11 +2433,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         if (Desktop.jalviewClipboard != null
                 && Desktop.jalviewClipboard[2] != null)
         {
-          List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
-          for (int[] region : hc)
-          {
-            af.viewport.hideColumns(region[0], region[1]);
-          }
+          HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
+          af.viewport.setHiddenColumns(hc);
         }
 
         // >>>This is a fix for the moment, until a better solution is
@@ -2251,7 +2472,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       System.out.println("Exception whilst pasting: " + ex);
       // could be anything being pasted in here
     }
-
   }
 
   @Override
@@ -2268,11 +2488,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       if (Desktop.jalviewClipboard != null
               && Desktop.jalviewClipboard[2] != null)
       {
-        List<int[]> hc = (List<int[]>) Desktop.jalviewClipboard[2];
-        for (int region[] : hc)
-        {
-          af.viewport.hideColumns(region[0], region[1]);
-        }
+        HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
+        af.viewport.setHiddenColumns(hc);
       }
 
       // >>>This is a fix for the moment, until a better solution is
@@ -4554,6 +4771,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param file
    *          either a filename or a URL string.
+   * @throws InterruptedException
+   * @throws IOException
    */
   public void loadJalviewDataFile(String file, DataSourceType sourceType,
           FileFormatI format, SequenceI assocSeq)
@@ -4641,11 +4860,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             new JnetAnnotationMaker();
             JnetAnnotationMaker.add_annotation(predictions,
                     viewport.getAlignment(), 0, false);
-            SequenceI repseq = viewport.getAlignment().getSequenceAt(0);
-            viewport.getAlignment().setSeqrep(repseq);
-            HiddenColumns cs = new HiddenColumns();
-            cs.hideInsertionsFor(repseq);
-            viewport.getAlignment().setHiddenColumns(cs);
+            viewport.getAlignment().setupJPredAlignment();
             isAnnotation = true;
           }
           // else if (IdentifyFile.FeaturesFile.equals(format))
@@ -4664,7 +4879,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       }
       if (isAnnotation)
       {
-
         alignPanel.adjustAnnotationHeight();
         viewport.updateSequenceIdColours();
         buildSortByAnnotationScoresMenu();
@@ -4867,14 +5081,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             MessageManager.getString("option.trim_retrieved_seqs"));
     trimrs.setToolTipText(
             MessageManager.getString("label.trim_retrieved_sequences"));
-    trimrs.setSelected(Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true));
+    trimrs.setSelected(
+            Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
     trimrs.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
         trimrs.setSelected(trimrs.isSelected());
-        Cache.setProperty("TRIM_FETCHED_DATASET_SEQS",
+        Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
                 Boolean.valueOf(trimrs.isSelected()).toString());
       };
     });
@@ -5588,6 +5803,68 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
   }
 
+  /**
+   * Sets the status of the HMMER menu
+   */
+  public void updateHMMERStatus()
+  {
+    hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable());
+  }
+
+  /**
+   * Returns the selected hidden Markov model.
+   * 
+   * @return
+   */
+  public HiddenMarkovModel getSelectedHMM()
+  {
+    if (selectedHMMSequence == null)
+    {
+      return null;
+    }
+    return selectedHMMSequence.getHMM();
+  }
+
+  /**
+   * Returns the selected hidden Markov model.
+   * 
+   * @return
+   */
+  public SequenceI getSelectedHMMSequence()
+  {
+    return selectedHMMSequence;
+  }
+
+  /**
+   * Sets the selected hidden Markov model
+   * 
+   * @param selectedHMM
+   */
+  public void setSelectedHMMSequence(SequenceI selectedHMM)
+  {
+    this.selectedHMMSequence = selectedHMM;
+    hmmAlign.setText(MessageManager.getString("label.hmmalign") + " to "
+            + selectedHMM.getHMM().getName());
+    hmmSearch.setText(MessageManager.getString("label.hmmsearch") + " with "
+            + selectedHMM.getHMM().getName());
+  }
+
+  @Override
+  public void hmmerMenu_actionPerformed(ActionEvent e)
+  {
+    SequenceGroup grp = getViewport().getSelectionGroup();
+    if (grp != null)
+    {
+      hmmBuild.setText(MessageManager.getString("label.hmmbuild") + " from "
+              + grp.getName());
+    }
+    else
+    {
+      hmmBuild.setText(MessageManager.getString("label.hmmbuild")
+              + " from Alignment");
+    }
+  }
+
   @Override
   protected void loadVcf_actionPerformed()
   {
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 4d09084..862c4fb 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -22,7 +22,6 @@ package jalview.gui;
 
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
-import jalview.analysis.TreeModel;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureColourI;
@@ -36,7 +35,6 @@ import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceGroup;
@@ -58,10 +56,9 @@ import java.awt.Dimension;
 import java.awt.Font;
 import java.awt.FontMetrics;
 import java.awt.Rectangle;
-import java.util.ArrayList;
 import java.util.Hashtable;
+import java.util.Iterator;
 import java.util.List;
-import java.util.Vector;
 
 import javax.swing.JInternalFrame;
 
@@ -95,6 +92,12 @@ public class AlignViewport extends AlignmentViewport
 
   private AnnotationColumnChooser annotationColumnSelectionState;
 
+  boolean validCharWidth;
+
+  public boolean followSelection = true;
+
+  private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
+
   /**
    * Creates a new AlignViewport object.
    * 
@@ -257,14 +260,14 @@ public class AlignViewport extends AlignmentViewport
 
     setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true);
 
-    alignment
-            .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
+    AlignmentI al = getAlignment();
+    al.setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
 
     // We must set conservation and consensus before setting colour,
     // as Blosum and Clustal require this to be done
-    if (hconsensus == null && !isDataset)
+    if (consensusProfiles == null && !isDataset)
     {
-      if (!alignment.isNucleotide())
+      if (!al.isNucleotide())
       {
         showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
         showQuality = Cache.getDefault("SHOW_QUALITY", true);
@@ -276,13 +279,19 @@ public class AlignViewport extends AlignmentViewport
       showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false);
       normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO",
               false);
+      // for now, use consensus options for Information till it gets its own
+      setShowHMMSequenceLogo(showSequenceLogo);
+      setNormaliseHMMSequenceLogo(normaliseSequenceLogo);
+      setShowInformationHistogram(showConsensusHistogram);
       showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
       showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
 
       showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true);
     }
     initAutoAnnotation();
-    String colourProperty = alignment.isNucleotide()
+    // initInformation();
+
+    String colourProperty = al.isNucleotide()
             ? Preferences.DEFAULT_COLOUR_NUC
             : Preferences.DEFAULT_COLOUR_PROT;
     String schemeName = Cache.getProperty(colourProperty);
@@ -293,7 +302,7 @@ public class AlignViewport extends AlignmentViewport
               ResidueColourScheme.NONE);
     }
     ColourSchemeI colourScheme = ColourSchemeProperty
-            .getColourScheme(alignment, schemeName);
+            .getColourScheme(al, schemeName);
     residueShading = new ResidueShader(colourScheme);
 
     if (colourScheme instanceof UserColourScheme)
@@ -305,12 +314,10 @@ public class AlignViewport extends AlignmentViewport
 
     if (residueShading != null)
     {
-      residueShading.setConsensus(hconsensus);
+      residueShading.setConsensus(consensusProfiles);
     }
   }
 
-  boolean validCharWidth;
-
   /**
    * {@inheritDoc}
    */
@@ -393,9 +400,9 @@ public class AlignViewport extends AlignmentViewport
     /*
      * replace mappings on our alignment
      */
-    if (alignment != null && align != null)
+    if (getAlignment() != null && align != null)
     {
-      alignment.setCodonFrames(align.getCodonFrames());
+      getAlignment().setCodonFrames(align.getCodonFrames());
     }
   }
 
@@ -446,17 +453,17 @@ public class AlignViewport extends AlignmentViewport
   }
 
   /**
-   * returns the visible column regions of the alignment
+   * Returns an iterator over the visible column regions of the alignment
    * 
    * @param selectedRegionOnly
    *          true to just return the contigs intersecting with the selected
    *          area
    * @return
    */
-  public int[] getViewAsVisibleContigs(boolean selectedRegionOnly)
+  public Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly)
   {
-    int[] viscontigs = null;
-    int start = 0, end = 0;
+    int start = 0;
+    int end = 0;
     if (selectedRegionOnly && selectionGroup != null)
     {
       start = selectionGroup.getStartRes();
@@ -464,10 +471,11 @@ public class AlignViewport extends AlignmentViewport
     }
     else
     {
-      end = alignment.getWidth();
+      end = getAlignment().getWidth();
     }
-    viscontigs = alignment.getHiddenColumns().getVisibleContigs(start, end);
-    return viscontigs;
+
+    return getAlignment().getHiddenColumns().getVisContigsIterator(start,
+            end, false);
   }
 
   /**
@@ -516,8 +524,6 @@ public class AlignViewport extends AlignmentViewport
     return false;
   }
 
-  public boolean followSelection = true;
-
   /**
    * @return true if view selection should always follow the selections
    *         broadcast by other selection sources
@@ -583,17 +589,6 @@ public class AlignViewport extends AlignmentViewport
             .getStructureSelectionManager(Desktop.instance);
   }
 
-  @Override
-  public boolean isNormaliseSequenceLogo()
-  {
-    return normaliseSequenceLogo;
-  }
-
-  public void setNormaliseSequenceLogo(boolean state)
-  {
-    normaliseSequenceLogo = state;
-  }
-
   /**
    * 
    * @return true if alignment characters should be displayed
@@ -604,8 +599,6 @@ public class AlignViewport extends AlignmentViewport
     return validCharWidth;
   }
 
-  private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<String, AutoCalcSetting>();
-
   public AutoCalcSetting getCalcIdSettingsFor(String calcId)
   {
     return calcIdParams.get(calcId);
@@ -1035,4 +1028,5 @@ public class AlignViewport extends AlignmentViewport
     }
     fr.setTransparency(featureSettings.getTransparency());
   }
+
 }
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 3a1dbe8..f5634d2 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -419,8 +419,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
     if (av.hasHiddenColumns())
     {
       HiddenColumns hidden = av.getAlignment().getHiddenColumns();
-      start = hidden.findColumnPosition(start);
-      end = hidden.findColumnPosition(end);
+      start = hidden.absoluteToVisibleColumn(start);
+      end = hidden.absoluteToVisibleColumn(end);
       if (start == end)
       {
         if (!hidden.isVisible(r[0]))
@@ -678,7 +678,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       {
         // reset the width to exclude hidden columns
         width = av.getAlignment().getHiddenColumns()
-                .findColumnPosition(width);
+                .absoluteToVisibleColumn(width);
       }
 
       hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
@@ -874,15 +874,17 @@ public class AlignmentPanel extends GAlignmentPanel implements
   @Override
   public void paintComponent(Graphics g)
   {
-    invalidate();
+    invalidate(); // needed so that the id width adjuster works correctly
 
     Dimension d = getIdPanel().getIdCanvas().getPreferredSize();
     idPanelHolder.setPreferredSize(d);
     hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
-    validate();
+
+    validate(); // needed so that the id width adjuster works correctly
 
     /*
-     * set scroll bar positions
+     * set scroll bar positions - tried to remove but necessary for split panel to resize correctly
+     * though I still think this call should be elsewhere.
      */
     ViewportRanges ranges = av.getRanges();
     setScrollValues(ranges.getStartRes(), ranges.getStartSeq());
@@ -1174,7 +1176,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     if (av.hasHiddenColumns())
     {
       maxwidth = av.getAlignment().getHiddenColumns()
-              .findColumnPosition(maxwidth) - 1;
+              .absoluteToVisibleColumn(maxwidth) - 1;
     }
 
     int resWidth = getSeqPanel().seqCanvas
@@ -1366,7 +1368,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     if (av.hasHiddenColumns())
     {
       maxwidth = av.getAlignment().getHiddenColumns()
-              .findColumnPosition(maxwidth);
+              .absoluteToVisibleColumn(maxwidth);
     }
 
     int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight())
@@ -1584,7 +1586,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     if (av.hasHiddenColumns())
     {
       maxwidth = av.getAlignment().getHiddenColumns()
-              .findColumnPosition(maxwidth) - 1;
+              .absoluteToVisibleColumn(maxwidth) - 1;
     }
 
     int height = ((maxwidth / chunkWidth) + 1) * cHeight;
@@ -1813,35 +1815,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   protected void scrollToCentre(SearchResultsI sr, int verticalOffset)
   {
-    /*
-     * To avoid jumpy vertical scrolling (if some sequences are gapped or not
-     * mapped), we can make the scroll-to location a sequence above the one
-     * actually mapped.
-     */
-    SequenceI mappedTo = sr.getResults().get(0).getSequence();
-    List<SequenceI> seqs = av.getAlignment().getSequences();
-
-    /*
-     * This is like AlignmentI.findIndex(seq) but here we are matching the
-     * dataset sequence not the aligned sequence
-     */
-    boolean matched = false;
-    for (SequenceI seq : seqs)
-    {
-      if (mappedTo == seq.getDatasetSequence())
-      {
-        matched = true;
-        break;
-      }
-    }
-    if (!matched)
-    {
-      return; // failsafe, shouldn't happen
-    }
-
-    /*
-     * Scroll to position but centring the target residue.
-     */
     scrollToPosition(sr, verticalOffset, true, true);
   }
 
diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 4e181b3..b1a8aff 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -25,6 +25,7 @@ import jalview.analysis.AlignmentUtils;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
@@ -33,6 +34,7 @@ import jalview.io.FormatAdapter;
 import jalview.util.Comparison;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
+import jalview.workers.InformationThread;
 
 import java.awt.Color;
 import java.awt.Cursor;
@@ -41,8 +43,6 @@ import java.awt.Font;
 import java.awt.FontMetrics;
 import java.awt.Graphics;
 import java.awt.Graphics2D;
-import java.awt.Image;
-import java.awt.MediaTracker;
 import java.awt.RenderingHints;
 import java.awt.Toolkit;
 import java.awt.datatransfer.StringSelection;
@@ -52,10 +52,9 @@ import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
 import java.awt.geom.AffineTransform;
-import java.awt.image.BufferedImage;
-import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
+import java.util.Iterator;
 import java.util.regex.Pattern;
 
 import javax.swing.JCheckBoxMenuItem;
@@ -73,9 +72,16 @@ import javax.swing.ToolTipManager;
 public class AnnotationLabels extends JPanel
         implements MouseListener, MouseMotionListener, ActionListener
 {
-  // width in pixels within which height adjuster arrows are shown and active
+  /**
+   * width in pixels within which height adjuster arrows are shown and active
+   */
   private static final int HEIGHT_ADJUSTER_WIDTH = 50;
 
+  /**
+   * height in pixels for allowing height adjuster to be active
+   */
+  private static int HEIGHT_ADJUSTER_HEIGHT = 10;
+
   private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern
           .compile("<");
 
@@ -105,10 +111,6 @@ public class AnnotationLabels extends JPanel
   private static final String COPYCONS_SEQ = MessageManager
           .getString("label.copy_consensus_sequence");
 
-  private static Image adjusterImage;
-
-  private static int adjusterImageHeight;
-
   private final boolean debugRedraw = false;
 
   private AlignmentPanel ap;
@@ -138,11 +140,6 @@ public class AnnotationLabels extends JPanel
     av = ap.av;
     ToolTipManager.sharedInstance().registerComponent(this);
 
-    if (adjusterImage == null)
-    {
-      loadAdjusterImage();
-    }
-
     addMouseListener(this);
     addMouseMotionListener(this);
     addMouseWheelListener(ap.getAnnotationPanel());
@@ -154,37 +151,6 @@ public class AnnotationLabels extends JPanel
   }
 
   /**
-   * Loads the gif for the panel height adjustment
-   */
-  protected void loadAdjusterImage()
-  {
-    java.net.URL url = getClass().getResource("/images/idwidth.gif");
-    Image temp = null;
-
-    if (url != null)
-    {
-      temp = Toolkit.getDefaultToolkit().createImage(url);
-    }
-
-    try
-    {
-      MediaTracker mt = new MediaTracker(this);
-      mt.addImage(temp, 0);
-      mt.waitForID(0);
-    } catch (Exception ex)
-    {
-    }
-
-    BufferedImage bi = new BufferedImage(temp.getHeight(this),
-            temp.getWidth(this), BufferedImage.TYPE_INT_RGB);
-    Graphics2D g = (Graphics2D) bi.getGraphics();
-    g.rotate(Math.toRadians(90));
-    g.drawImage(temp, 0, -bi.getWidth(this), this);
-    adjusterImage = bi;
-    adjusterImageHeight = bi.getHeight();
-  }
-
-  /**
    * DOCUMENT ME!
    * 
    * @param y
@@ -387,6 +353,10 @@ public class AnnotationLabels extends JPanel
       pop.show(this, evt.getX(), evt.getY());
       return;
     }
+
+    final AlignmentAnnotation ann = aa[selectedRow];
+    final boolean isSequenceAnnotation = ann.sequenceRef != null;
+
     item = new JMenuItem(EDITNAME);
     item.addActionListener(this);
     pop.add(item);
@@ -396,9 +366,9 @@ public class AnnotationLabels extends JPanel
     // JAL-1264 hide all sequence-specific annotations of this type
     if (selectedRow < aa.length)
     {
-      if (aa[selectedRow].sequenceRef != null)
+      if (isSequenceAnnotation)
       {
-        final String label = aa[selectedRow].label;
+        final String label = ann.label;
         JMenuItem hideType = new JMenuItem();
         String text = MessageManager.getString("label.hide_all") + " "
                 + label;
@@ -411,15 +381,6 @@ public class AnnotationLabels extends JPanel
             AlignmentUtils.showOrHideSequenceAnnotations(
                     ap.av.getAlignment(), Collections.singleton(label),
                     null, false, false);
-            // for (AlignmentAnnotation ann : ap.av.getAlignment()
-            // .getAlignmentAnnotation())
-            // {
-            // if (ann.sequenceRef != null && ann.label != null
-            // && ann.label.equals(label))
-            // {
-            // ann.visible = false;
-            // }
-            // }
             ap.refresh(true);
           }
         });
@@ -442,190 +403,317 @@ public class AnnotationLabels extends JPanel
     // property methods
     if (selectedRow < aa.length)
     {
-      final String label = aa[selectedRow].label;
-      if (!aa[selectedRow].autoCalculated)
+      final String label = ann.label;
+      if (!(ann.autoCalculated)
+              && !(InformationThread.HMM_CALC_ID.equals(ann.getCalcId())))
       {
-        if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH)
+        if (ann.graph == AlignmentAnnotation.NO_GRAPH)
         {
           // display formatting settings for this row.
           pop.addSeparator();
           // av and sequencegroup need to implement same interface for
           item = new JCheckBoxMenuItem(TOGGLE_LABELSCALE,
-                  aa[selectedRow].scaleColLabel);
+                  ann.scaleColLabel);
           item.addActionListener(this);
           pop.add(item);
         }
       }
       else if (label.indexOf("Consensus") > -1)
       {
-        pop.addSeparator();
-        // av and sequencegroup need to implement same interface for
-        final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
-                MessageManager.getString("label.ignore_gaps_consensus"),
-                (aa[selectedRow].groupRef != null)
-                        ? aa[selectedRow].groupRef.getIgnoreGapsConsensus()
-                        : ap.av.isIgnoreGapsConsensus());
-        final AlignmentAnnotation aaa = aa[selectedRow];
-        cbmi.addActionListener(new ActionListener()
+        addConsensusMenu(pop, ann);
+      }
+      else if (InformationThread.HMM_CALC_ID.equals(ann.getCalcId()))
+      {
+        addHmmerMenu(pop, ann);
+      }
+    }
+    pop.show(this, evt.getX(), evt.getY());
+  }
+
+  /**
+   * Adds context menu options for (alignment or group) Hmmer annotation
+   * 
+   * @param pop
+   * @param ann
+   */
+  protected void addHmmerMenu(JPopupMenu pop, final AlignmentAnnotation ann)
+  {
+    final boolean isGroupAnnotation = ann.groupRef != null;
+    pop.addSeparator();
+    final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
+            MessageManager.getString(
+                    "label.ignore_below_background_frequency"),
+            isGroupAnnotation
+                    ? ann.groupRef
+                            .isIgnoreBelowBackground()
+                    : ap.av.isIgnoreBelowBackground());
+    cbmi.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        if (isGroupAnnotation)
         {
-          @Override
-          public void actionPerformed(ActionEvent e)
+          if (!ann.groupRef.isUseInfoLetterHeight())
           {
-            if (aaa.groupRef != null)
-            {
-              // TODO: pass on reference to ap so the view can be updated.
-              aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
-              ap.getAnnotationPanel()
-                      .paint(ap.getAnnotationPanel().getGraphics());
-            }
-            else
-            {
-              ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
-            }
-            ap.alignmentChanged();
+            ann.groupRef.setIgnoreBelowBackground(cbmi.getState());
+            // todo and recompute group annotation
           }
-        });
-        pop.add(cbmi);
-        // av and sequencegroup need to implement same interface for
-        if (aaa.groupRef != null)
+        }
+        else if (!ap.av.isInfoLetterHeight())
         {
-          final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
-                  MessageManager.getString("label.show_group_histogram"),
-                  aa[selectedRow].groupRef.isShowConsensusHistogram());
-          chist.addActionListener(new ActionListener()
-          {
-            @Override
-            public void actionPerformed(ActionEvent e)
-            {
-              // TODO: pass on reference
-              // to ap
-              // so the
-              // view
-              // can be
-              // updated.
-              aaa.groupRef.setShowConsensusHistogram(chist.getState());
-              ap.repaint();
-              // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
-            }
-          });
-          pop.add(chist);
-          final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
-                  MessageManager.getString("label.show_group_logo"),
-                  aa[selectedRow].groupRef.isShowSequenceLogo());
-          cprofl.addActionListener(new ActionListener()
-          {
-            @Override
-            public void actionPerformed(ActionEvent e)
-            {
-              // TODO: pass on reference
-              // to ap
-              // so the
-              // view
-              // can be
-              // updated.
-              aaa.groupRef.setshowSequenceLogo(cprofl.getState());
-              ap.repaint();
-              // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
-            }
-          });
-          pop.add(cprofl);
-          final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
-                  MessageManager.getString("label.normalise_group_logo"),
-                  aa[selectedRow].groupRef.isNormaliseSequenceLogo());
-          cproflnorm.addActionListener(new ActionListener()
-          {
-            @Override
-            public void actionPerformed(ActionEvent e)
-            {
+          ap.av.setIgnoreBelowBackground(cbmi.getState(), ap);
+          // todo and recompute annotation
+        }
+        ap.alignmentChanged(); // todo not like this
+      }
+    });
+    pop.add(cbmi);
+    final JCheckBoxMenuItem letterHeight = new JCheckBoxMenuItem(
+            MessageManager.getString("label.use_info_for_height"),
+            isGroupAnnotation ? ann.groupRef.isUseInfoLetterHeight()
+                    : ap.av.isInfoLetterHeight());
+    letterHeight.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        if (isGroupAnnotation)
+        {
+          ann.groupRef.setInfoLetterHeight((letterHeight.getState()));
+          ann.groupRef.setIgnoreBelowBackground(true);
+          // todo and recompute group annotation
+        }
+        else
+        {
+          ap.av.setInfoLetterHeight(letterHeight.getState(), ap);
+          ap.av.setIgnoreBelowBackground(true, ap);
+          // todo and recompute annotation
+        }
+        ap.alignmentChanged();
+      }
+    });
+    pop.add(letterHeight);
+    if (isGroupAnnotation)
+    {
+      final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+              MessageManager.getString("label.show_group_histogram"),
+              ann.groupRef.isShowInformationHistogram());
+      chist.addActionListener(new ActionListener()
+      {
+        @Override
+        public void actionPerformed(ActionEvent e)
+        {
+          ann.groupRef.setShowInformationHistogram(chist.getState());
+          ap.repaint();
+        }
+      });
+      pop.add(chist);
+      final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
+              MessageManager.getString("label.show_group_logo"),
+              ann.groupRef.isShowHMMSequenceLogo());
+      cprofl.addActionListener(new ActionListener()
+      {
+        @Override
+        public void actionPerformed(ActionEvent e)
+        {
+          ann.groupRef.setShowHMMSequenceLogo(cprofl.getState());
+          ap.repaint();
+        }
+      });
+      pop.add(cprofl);
+      final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
+              MessageManager.getString("label.normalise_group_logo"),
+              ann.groupRef.isNormaliseHMMSequenceLogo());
+      cproflnorm.addActionListener(new ActionListener()
+      {
+        @Override
+        public void actionPerformed(ActionEvent e)
+        {
+          ann.groupRef
+                  .setNormaliseHMMSequenceLogo(cproflnorm.getState());
+          // automatically enable logo display if we're clicked
+          ann.groupRef.setShowHMMSequenceLogo(true);
+          ap.repaint();
+        }
+      });
+      pop.add(cproflnorm);
+    }
+    else
+    {
+      final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+              MessageManager.getString("label.show_histogram"),
+              av.isShowInformationHistogram());
+      chist.addActionListener(new ActionListener()
+      {
+        @Override
+        public void actionPerformed(ActionEvent e)
+        {
+          av.setShowInformationHistogram(chist.getState());
+          ap.repaint();
+        }
+      });
+      pop.add(chist);
+      final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
+              MessageManager.getString("label.show_logo"),
+              av.isShowHMMSequenceLogo());
+      cprof.addActionListener(new ActionListener()
+      {
+        @Override
+        public void actionPerformed(ActionEvent e)
+        {
+          av.setShowHMMSequenceLogo(cprof.getState());
+          ap.repaint();
+        }
+      });
+      pop.add(cprof);
+      final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
+              MessageManager.getString("label.normalise_logo"),
+              av.isNormaliseHMMSequenceLogo());
+      cprofnorm.addActionListener(new ActionListener()
+      {
+        @Override
+        public void actionPerformed(ActionEvent e)
+        {
+          av.setShowHMMSequenceLogo(true);
+          av.setNormaliseHMMSequenceLogo(cprofnorm.getState());
+          ap.repaint();
+        }
+      });
+      pop.add(cprofnorm);
+    }
+  }
 
-              // TODO: pass on reference
-              // to ap
-              // so the
-              // view
-              // can be
-              // updated.
-              aaa.groupRef.setNormaliseSequenceLogo(cproflnorm.getState());
-              // automatically enable logo display if we're clicked
-              aaa.groupRef.setshowSequenceLogo(true);
-              ap.repaint();
-              // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
-            }
-          });
-          pop.add(cproflnorm);
+  /**
+   * Adds context menu options for (alignment or group) Consensus annotation
+   * 
+   * @param pop
+   * @param ann
+   */
+  protected void addConsensusMenu(JPopupMenu pop,
+          final AlignmentAnnotation ann)
+  {
+    final boolean isGroupAnnotation = ann.groupRef != null;
+    pop.addSeparator();
+
+    final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
+            MessageManager.getString("label.ignore_gaps_consensus"),
+            (ann.groupRef != null)
+                    ? ann.groupRef.isIgnoreGapsConsensus()
+                    : ap.av.isIgnoreGapsConsensus());
+    cbmi.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        if (isGroupAnnotation)
+        {
+          ann.groupRef.setIgnoreGapsConsensus(cbmi.getState());
         }
         else
         {
-          final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
-                  MessageManager.getString("label.show_histogram"),
-                  av.isShowConsensusHistogram());
-          chist.addActionListener(new ActionListener()
-          {
-            @Override
-            public void actionPerformed(ActionEvent e)
-            {
-              // TODO: pass on reference
-              // to ap
-              // so the
-              // view
-              // can be
-              // updated.
-              av.setShowConsensusHistogram(chist.getState());
-              ap.alignFrame.setMenusForViewport();
-              ap.repaint();
-              // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
-            }
-          });
-          pop.add(chist);
-          final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
-                  MessageManager.getString("label.show_logo"),
-                  av.isShowSequenceLogo());
-          cprof.addActionListener(new ActionListener()
-          {
-            @Override
-            public void actionPerformed(ActionEvent e)
-            {
-              // TODO: pass on reference
-              // to ap
-              // so the
-              // view
-              // can be
-              // updated.
-              av.setShowSequenceLogo(cprof.getState());
-              ap.alignFrame.setMenusForViewport();
-              ap.repaint();
-              // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
-            }
-          });
-          pop.add(cprof);
-          final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
-                  MessageManager.getString("label.normalise_logo"),
-                  av.isNormaliseSequenceLogo());
-          cprofnorm.addActionListener(new ActionListener()
-          {
-            @Override
-            public void actionPerformed(ActionEvent e)
-            {
-              // TODO: pass on reference
-              // to ap
-              // so the
-              // view
-              // can be
-              // updated.
-              av.setShowSequenceLogo(true);
-              av.setNormaliseSequenceLogo(cprofnorm.getState());
-              ap.alignFrame.setMenusForViewport();
-              ap.repaint();
-              // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
-            }
-          });
-          pop.add(cprofnorm);
+          ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
         }
-        final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
-        consclipbrd.addActionListener(this);
-        pop.add(consclipbrd);
+        ap.alignmentChanged();
       }
+    });
+    pop.add(cbmi);
+    if (isGroupAnnotation)
+    {
+      /*
+       * group consensus options
+       */
+      final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+              MessageManager.getString("label.show_group_histogram"),
+              ann.groupRef.isShowConsensusHistogram());
+      chist.addActionListener(new ActionListener()
+      {
+        @Override
+        public void actionPerformed(ActionEvent e)
+        {
+          ann.groupRef.setShowConsensusHistogram(chist.getState());
+          ap.repaint();
+        }
+      });
+      pop.add(chist);
+      final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
+              MessageManager.getString("label.show_group_logo"),
+              ann.groupRef.isShowSequenceLogo());
+      cprofl.addActionListener(new ActionListener()
+      {
+        @Override
+        public void actionPerformed(ActionEvent e)
+        {
+          ann.groupRef.setshowSequenceLogo(cprofl.getState());
+          ap.repaint();
+        }
+      });
+      pop.add(cprofl);
+      final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
+              MessageManager.getString("label.normalise_group_logo"),
+              ann.groupRef.isNormaliseSequenceLogo());
+      cproflnorm.addActionListener(new ActionListener()
+      {
+        @Override
+        public void actionPerformed(ActionEvent e)
+        {
+          ann.groupRef.setNormaliseSequenceLogo(cproflnorm.getState());
+          // automatically enable logo display if we're clicked
+          ann.groupRef.setshowSequenceLogo(true);
+          ap.repaint();
+        }
+      });
+      pop.add(cproflnorm);
     }
-    pop.show(this, evt.getX(), evt.getY());
+    else
+    {
+      /*
+       * alignment consensus options
+       */
+      final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+              MessageManager.getString("label.show_histogram"),
+              av.isShowConsensusHistogram());
+      chist.addActionListener(new ActionListener()
+      {
+        @Override
+        public void actionPerformed(ActionEvent e)
+        {
+          av.setShowConsensusHistogram(chist.getState());
+          ap.repaint();
+        }
+      });
+      pop.add(chist);
+      final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
+              MessageManager.getString("label.show_logo"),
+              av.isShowSequenceLogo());
+      cprof.addActionListener(new ActionListener()
+      {
+        @Override
+        public void actionPerformed(ActionEvent e)
+        {
+          av.setShowSequenceLogo(cprof.getState());
+          ap.repaint();
+        }
+      });
+      pop.add(cprof);
+      final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
+              MessageManager.getString("label.normalise_logo"),
+              av.isNormaliseSequenceLogo());
+      cprofnorm.addActionListener(new ActionListener()
+      {
+        @Override
+        public void actionPerformed(ActionEvent e)
+        {
+          av.setShowSequenceLogo(true);
+          av.setNormaliseSequenceLogo(cprofnorm.getState());
+          ap.repaint();
+        }
+      });
+      pop.add(cprofnorm);
+    }
+    final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
+    consclipbrd.addActionListener(this);
+    pop.add(consclipbrd);
   }
 
   /**
@@ -816,7 +904,7 @@ public class AnnotationLabels extends JPanel
   protected void showOrHideAdjuster(MouseEvent evt)
   {
     boolean was = resizePanel;
-    resizePanel = evt.getY() < adjusterImageHeight && evt.getX() < HEIGHT_ADJUSTER_WIDTH;
+    resizePanel = evt.getY() < HEIGHT_ADJUSTER_HEIGHT && evt.getX() < HEIGHT_ADJUSTER_WIDTH;
 
     if (resizePanel != was)
     {
@@ -939,7 +1027,6 @@ public class AnnotationLabels extends JPanel
             PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
             ap.av.sendSelection();
           }
-
         }
       }
       return;
@@ -968,8 +1055,9 @@ public class AnnotationLabels extends JPanel
     Alignment ds = new Alignment(dseqs);
     if (av.hasHiddenColumns())
     {
-      omitHidden = av.getAlignment().getHiddenColumns()
-              .getVisibleSequenceStrings(0, sq.getLength(), seqs);
+      Iterator<int[]> it = av.getAlignment().getHiddenColumns()
+              .getVisContigsIterator(0, sq.getLength(), false);
+      omitHidden = new String[] { sq.getSequenceStringFromIterator(it) };
     }
 
     int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 };
@@ -985,12 +1073,12 @@ public class AnnotationLabels extends JPanel
     Toolkit.getDefaultToolkit().getSystemClipboard()
             .setContents(new StringSelection(output), Desktop.instance);
 
-    ArrayList<int[]> hiddenColumns = null;
+    HiddenColumns hiddenColumns = null;
 
     if (av.hasHiddenColumns())
     {
-      hiddenColumns = av.getAlignment().getHiddenColumns()
-              .getHiddenColumnsCopy();
+      hiddenColumns = new HiddenColumns(
+              av.getAlignment().getHiddenColumns());
     }
 
     Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset
@@ -1010,7 +1098,6 @@ public class AnnotationLabels extends JPanel
   @Override
   public void paintComponent(Graphics g)
   {
-
     int width = getWidth();
     if (width == 0)
     {
@@ -1025,7 +1112,6 @@ public class AnnotationLabels extends JPanel
     }
 
     drawComponent(g2, true, width);
-
   }
 
   /**
@@ -1225,11 +1311,7 @@ public class AnnotationLabels extends JPanel
       }
     }
 
-    if (resizePanel)
-    {
-      // g.drawImage(adjusterImage, 2, 0 - getScrollOffset(), this);
-    }
-    else if (dragEvent != null && aa != null)
+    if (!resizePanel && dragEvent != null && aa != null)
     {
       g.setColor(Color.lightGray);
       g.drawString(aa[selectedRow].label, dragEvent.getX(),
diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 438e81b..dee56b0 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -175,11 +175,12 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     if (e.isShiftDown())
     {
       e.consume();
-      if (e.getWheelRotation() > 0)
+      double wheelRotation = e.getPreciseWheelRotation();
+      if (wheelRotation > 0)
       {
         av.getRanges().scrollRight(true);
       }
-      else
+      else if (wheelRotation < 0)
       {
         av.getRanges().scrollRight(false);
       }
@@ -724,7 +725,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     if (av.hasHiddenColumns())
     {
       column = av.getAlignment().getHiddenColumns()
-              .adjustForHiddenColumns(column);
+              .visibleToAbsoluteColumn(column);
     }
 
     AlignmentAnnotation ann = aa[row];
@@ -782,6 +783,10 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       {
         this.setToolTipText(JvSwingUtils.wrapTooltip(true, description));
       }
+      else
+      {
+        this.setToolTipText(null); // no tooltip if null or empty description
+      }
     }
     else
     {
@@ -904,6 +909,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   @Override
   public void paintComponent(Graphics g)
   {
+    super.paintComponent(g);
+
     g.setColor(Color.white);
     g.fillRect(0, 0, getWidth(), getHeight());
 
@@ -959,7 +966,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       gg.fillRect(0, 0, imgWidth, image.getHeight());
       imageFresh = true;
     }
-
+    
     drawComponent(gg, av.getRanges().getStartRes(),
             av.getRanges().getEndRes() + 1);
     imageFresh = false;
@@ -992,10 +999,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     int er = av.getRanges().getEndRes() + 1;
     int transX = 0;
 
-    long stime = System.currentTimeMillis();
     gg.copyArea(0, 0, imgWidth, getHeight(),
             -horizontal * av.getCharWidth(), 0);
-    long mtime = System.currentTimeMillis();
 
     if (horizontal > 0) // scrollbar pulled right, image to the left
     {
@@ -1012,17 +1017,13 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     drawComponent(gg, sr, er);
 
     gg.translate(-transX, 0);
-    long dtime = System.currentTimeMillis();
+
     fastPaint = true;
-    repaint();
-    long rtime = System.currentTimeMillis();
-    if (debugRedraw)
-    {
-      System.err.println("Scroll:\t" + horizontal + "\tCopyArea:\t"
-              + (mtime - stime) + "\tDraw component:\t" + (dtime - mtime)
-              + "\tRepaint call:\t" + (rtime - dtime));
-    }
 
+    // Call repaint on alignment panel so that repaints from other alignment
+    // panel components can be aggregated. Otherwise performance of the overview
+    // window and others may be adversely affected.
+    av.getAlignPanel().repaint();
   }
 
   private volatile boolean lastImageGood = false;
diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java
index f674c7e..eaaf0a5 100644
--- a/src/jalview/gui/CalculationChooser.java
+++ b/src/jalview/gui/CalculationChooser.java
@@ -23,10 +23,12 @@ package jalview.gui;
 import jalview.analysis.TreeBuilder;
 import jalview.analysis.scoremodels.ScoreModels;
 import jalview.analysis.scoremodels.SimilarityParams;
+import jalview.api.AlignViewportI;
 import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.SimilarityParamsI;
 import jalview.datamodel.SequenceGroup;
 import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
@@ -103,7 +105,7 @@ public class CalculationChooser extends JPanel
 
   final ComboBoxTooltipRenderer renderer = new ComboBoxTooltipRenderer();
 
-  List<String> tips = new ArrayList<String>();
+  List<String> tips = new ArrayList<>();
 
   /*
    * the most recently opened PCA results panel
@@ -375,7 +377,7 @@ public class CalculationChooser extends JPanel
    */
   protected JComboBox<String> buildModelOptionsList()
   {
-    final JComboBox<String> scoreModelsCombo = new JComboBox<String>();
+    final JComboBox<String> scoreModelsCombo = new JComboBox<>();
     scoreModelsCombo.setRenderer(renderer);
 
     /*
@@ -418,7 +420,7 @@ public class CalculationChooser extends JPanel
   {
     Object curSel = comboBox.getSelectedItem();
     toolTips.clear();
-    DefaultComboBoxModel<String> model = new DefaultComboBoxModel<String>();
+    DefaultComboBoxModel<String> model = new DefaultComboBoxModel<>();
 
     /*
      * now we can actually add entries to the combobox,
@@ -492,7 +494,7 @@ public class CalculationChooser extends JPanel
      * gui validation shouldn't allow insufficient sequences here, but leave
      * this check in in case this method gets exposed programmatically in future
      */
-    AlignViewport viewport = af.getViewport();
+    AlignViewportI viewport = af.getViewport();
     SequenceGroup sg = viewport.getSelectionGroup();
     if (sg != null && sg.getSize() < MIN_TREE_SELECTION)
     {
@@ -519,7 +521,7 @@ public class CalculationChooser extends JPanel
    */
   protected void openPcaPanel(String modelName, SimilarityParamsI params)
   {
-    AlignViewport viewport = af.getViewport();
+    AlignViewportI viewport = af.getViewport();
 
     /*
      * gui validation shouldn't allow insufficient sequences here, but leave
diff --git a/src/jalview/gui/ColourMenuHelper.java b/src/jalview/gui/ColourMenuHelper.java
index 8f0b88c..9479ea6 100644
--- a/src/jalview/gui/ColourMenuHelper.java
+++ b/src/jalview/gui/ColourMenuHelper.java
@@ -121,8 +121,7 @@ public class ColourMenuHelper
        */
       final String name = scheme.getSchemeName();
       String label = MessageManager.getStringOrReturn(
-              "label.colourScheme_" + name.toLowerCase().replace(" ", "_"),
-              name);
+              "label.colourScheme_", name.toLowerCase().replace(" ", "_"));
       final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
               label);
       radioItem.setName(name);
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 128481c..b26a8af 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -849,6 +849,7 @@ public class Desktop extends jalview.jbgui.GDesktop
     frame.setResizable(resizable);
     frame.setMaximizable(resizable);
     frame.setIconifiable(resizable);
+    frame.setOpaque(false);
 
     if (frame.getX() < 1 && frame.getY() < 1)
     {
@@ -899,8 +900,6 @@ public class Desktop extends jalview.jbgui.GDesktop
           menuItem.removeActionListener(menuItem.getActionListeners()[0]);
         }
         windowMenu.remove(menuItem);
-
-        System.gc();
       };
     });
 
@@ -1388,7 +1387,6 @@ public class Desktop extends jalview.jbgui.GDesktop
     {
       ssm.resetAll();
     }
-    System.gc();
   }
 
   @Override
@@ -1473,7 +1471,8 @@ public class Desktop extends jalview.jbgui.GDesktop
       return;
     }
 
-    AlignmentViewport source = null, target = null;
+    AlignViewportI source = null;
+    AlignViewportI target = null;
     if (frames[0] instanceof AlignFrame)
     {
       source = ((AlignFrame) frames[0]).getCurrentView();
diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 1dbc9b8..821454f 100644
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -1028,12 +1028,13 @@ public class FeatureSettings extends JPanel
 
   public void invertSelection()
   {
-    for (int i = 0; i < table.getRowCount(); i++)
+    Object[][] data = ((FeatureTableModel) table.getModel()).getData();
+    for (int i = 0; i < data.length; i++)
     {
-      Boolean value = (Boolean) table.getValueAt(i, SHOW_COLUMN);
-
-      table.setValueAt(new Boolean(!value.booleanValue()), i, SHOW_COLUMN);
+      data[i][SHOW_COLUMN] = !(Boolean) data[i][SHOW_COLUMN];
     }
+    updateFeatureRenderer(data, true);
+    table.repaint();
   }
 
   public void orderByAvWidth()
diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index 085b259..cd7b0b7 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -83,7 +83,7 @@ public class IdCanvas extends JPanel implements ViewportListenerI
     this.av = av;
     PaintRefresher.Register(this, av.getSequenceSetId());
     av.getRanges().addPropertyChangeListener(this);
-  }
+    }
 
   /**
    * DOCUMENT ME!
@@ -204,7 +204,11 @@ public class IdCanvas extends JPanel implements ViewportListenerI
     gg.translate(0, -transY);
 
     fastPaint = true;
-    repaint();
+
+    // Call repaint on alignment panel so that repaints from other alignment
+    // panel components can be aggregated. Otherwise performance of the overview
+    // window and others may be adversely affected.
+    av.getAlignPanel().repaint();
   }
 
   /**
@@ -216,41 +220,43 @@ public class IdCanvas extends JPanel implements ViewportListenerI
   @Override
   public void paintComponent(Graphics g)
   {
+    super.paintComponent(g);
+
     g.setColor(Color.white);
     g.fillRect(0, 0, getWidth(), getHeight());
-
+    
     if (fastPaint)
     {
       fastPaint = false;
       g.drawImage(image, 0, 0, this);
-
+    
       return;
     }
-
+    
     int oldHeight = imgHeight;
-
+    
     imgHeight = getHeight();
     imgHeight -= (imgHeight % av.getCharHeight());
-
+    
     if (imgHeight < 1)
     {
       return;
     }
-
+    
     if (oldHeight != imgHeight || image.getWidth(this) != getWidth())
     {
-      image = new BufferedImage(getWidth(), imgHeight,
-              BufferedImage.TYPE_INT_RGB);
+    	image = new BufferedImage(getWidth(), imgHeight,
+                BufferedImage.TYPE_INT_RGB);
     }
-
+    
     gg = (Graphics2D) image.getGraphics();
-
+    
     // Fill in the background
     gg.setColor(Color.white);
     gg.fillRect(0, 0, getWidth(), imgHeight);
-
+    
     drawIds(av.getRanges().getStartSeq(), av.getRanges().getEndSeq());
-
+    
     g.drawImage(image, 0, 0, this);
   }
 
@@ -374,7 +380,7 @@ public class IdCanvas extends JPanel implements ViewportListenerI
     if (av.hasHiddenColumns())
     {
       maxwidth = av.getAlignment().getHiddenColumns()
-              .findColumnPosition(maxwidth) - 1;
+              .absoluteToVisibleColumn(maxwidth) - 1;
     }
 
     int annotationHeight = 0;
diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index a1726f1..a183144 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -147,7 +147,8 @@ public class IdPanel extends JPanel
   public void mouseWheelMoved(MouseWheelEvent e)
   {
     e.consume();
-    if (e.getWheelRotation() > 0)
+    double wheelRotation = e.getPreciseWheelRotation();
+    if (wheelRotation > 0)
     {
       if (e.isShiftDown())
       {
@@ -158,7 +159,7 @@ public class IdPanel extends JPanel
         av.getRanges().scrollUp(false);
       }
     }
-    else
+    else if (wheelRotation < 0)
     {
       if (e.isShiftDown())
       {
diff --git a/src/jalview/gui/IdwidthAdjuster.java b/src/jalview/gui/IdwidthAdjuster.java
index 99792c6..0cffc3b 100755
--- a/src/jalview/gui/IdwidthAdjuster.java
+++ b/src/jalview/gui/IdwidthAdjuster.java
@@ -25,7 +25,6 @@ import jalview.api.AlignViewportI;
 import java.awt.Color;
 import java.awt.Cursor;
 import java.awt.Graphics;
-import java.awt.Image;
 import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
@@ -45,8 +44,6 @@ public class IdwidthAdjuster extends JPanel
 
   int oldX = 0;
 
-  Image image;
-
   AlignmentPanel ap;
 
   /**
@@ -58,14 +55,7 @@ public class IdwidthAdjuster extends JPanel
   public IdwidthAdjuster(AlignmentPanel ap)
   {
     this.ap = ap;
-
-    java.net.URL url = getClass().getResource("/images/idwidth.gif");
-
-    if (url != null)
-    {
-      image = java.awt.Toolkit.getDefaultToolkit().createImage(url);
-    }
-
+    setBackground(Color.white);
     addMouseListener(this);
     addMouseMotionListener(this);
   }
@@ -197,15 +187,7 @@ public class IdwidthAdjuster extends JPanel
 
     if (active)
     {
-      if (image != null)
-      {
-        // g.drawImage(image, getWidth() - 20, 2, this);
         setCursor(Cursor.getPredefinedCursor(Cursor.W_RESIZE_CURSOR));
-      }
-      else
-      {
-        setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
-      }
     }
   }
 }
diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index fdc2847..3840597 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1223,7 +1223,7 @@ public class Jalview2XML
         jGroup.setTextCol2(sg.textColour2.getRGB());
         jGroup.setTextColThreshold(sg.thresholdTextColour);
         jGroup.setShowUnconserved(sg.getShowNonconserved());
-        jGroup.setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
+        jGroup.setIgnoreGapsinConsensus(sg.isIgnoreGapsConsensus());
         jGroup.setShowConsensusHistogram(sg.isShowConsensusHistogram());
         jGroup.setShowSequenceLogo(sg.isShowSequenceLogo());
         jGroup.setNormaliseSequenceLogo(sg.isNormaliseSequenceLogo());
@@ -1450,9 +1450,10 @@ public class Jalview2XML
         }
         else
         {
-          ArrayList<int[]> hiddenRegions = hidden.getHiddenColumnsCopy();
-          for (int[] region : hiddenRegions)
+          Iterator<int[]> hiddenRegions = hidden.iterator();
+          while (hiddenRegions.hasNext())
           {
+            int[] region = hiddenRegions.next();
             HiddenColumns hc = new HiddenColumns();
             hc.setStart(region[0]);
             hc.setEnd(region[1]);
@@ -4560,7 +4561,7 @@ public class Jalview2XML
     af.viewport.getResidueShading().setThreshold(view.getPidThreshold(),
             view.getIgnoreGapsinConsensus());
     af.viewport.getResidueShading()
-            .setConsensus(af.viewport.getSequenceConsensusHash());
+            .setConsensus(af.viewport.getConsensusProfiles());
     af.viewport.setColourAppliesToAllGroups(false);
 
     if (view.getConservationSelected() && cs != null)
diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index 331e738..5cbf228 100755
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -413,7 +413,7 @@ public class Jalview2XML_V1
     af.viewport.getResidueShading().setThreshold(view.getPidThreshold(),
             true);
     af.viewport.getResidueShading()
-            .setConsensus(af.viewport.getSequenceConsensusHash());
+            .setConsensus(af.viewport.getConsensusProfiles());
     af.viewport.setColourAppliesToAllGroups(false);
     af.alignPanel.updateLayout();
     af.changeColour(cs);
diff --git a/src/jalview/gui/OptsAndParamsPage.java b/src/jalview/gui/OptsAndParamsPage.java
index 5342c90..1505df8 100644
--- a/src/jalview/gui/OptsAndParamsPage.java
+++ b/src/jalview/gui/OptsAndParamsPage.java
@@ -26,6 +26,7 @@ import jalview.ws.params.OptionI;
 import jalview.ws.params.ParameterI;
 import jalview.ws.params.ValueConstrainI;
 import jalview.ws.params.ValueConstrainI.ValueType;
+import jalview.ws.params.simple.LogarithmicParameter;
 
 import java.awt.BorderLayout;
 import java.awt.Component;
@@ -273,6 +274,9 @@ public class OptsAndParamsPage
   public class ParamBox extends JPanel
           implements ChangeListener, ActionListener, MouseListener
   {
+
+    boolean isLogarithmic;
+
     boolean adjusting = false;
 
     boolean choice = false;
@@ -325,6 +329,10 @@ public class OptsAndParamsPage
           choice = true;
         }
       }
+      if (parm instanceof LogarithmicParameter)
+      {
+        isLogarithmic = true;
+      }
 
       if (!compact)
       {
@@ -571,13 +579,34 @@ public class OptsAndParamsPage
     {
       if (!adjusting)
       {
-        valueField.setText("" + ((integ) ? ("" + slider.getValue())
-                : ("" + slider.getValue() / 1000f)));
+        if (!isLogarithmic)
+        {
+          valueField.setText("" + ((integ) ? ("" + slider.getValue())
+                  : ("" + slider.getValue() / 1000f)));
+        }
+        else
+        {
+          Double base = ((LogarithmicParameter) parameter).getBase();
+          Double value = Math.pow(
+                  base,
+                  slider.getValue() / 1000000f);
+          valueField.setText(formatDouble(value));
+        }
         checkIfModified();
       }
 
     }
 
+    public String formatDouble(Double value)
+    {
+      String string = String.format("%3.3f", value);
+      if (value < 0.001)
+      {
+        string = String.format("%3.3e", value);
+      }
+      return string;
+    }
+
     public void updateControls(ParameterI parm)
     {
       adjusting = true;
@@ -648,7 +677,17 @@ public class OptsAndParamsPage
         }
         else
         {
-          valueField.setText(parm.getValue());
+          if (parm instanceof LogarithmicParameter)
+          {
+            Double base = ((LogarithmicParameter) parm).getBase();
+            Double value = Math.pow(base,
+                    Double.parseDouble(parm.getValue()) / 1000000);
+            valueField.setText(formatDouble(value));
+          }
+          else
+          {
+            valueField.setText(parm.getValue());
+          }
         }
       }
       lastVal = updateSliderFromValueField();
@@ -659,6 +698,7 @@ public class OptsAndParamsPage
     {
       int iVal;
       float fVal;
+      double dVal;
       if (validator != null)
       {
         if (integ)
@@ -700,6 +740,54 @@ public class OptsAndParamsPage
           }
           return new int[] { iVal };
         }
+        else if (isLogarithmic)
+        {
+          double eValue;
+          dVal = 0d;
+          try
+          {
+            valueField.setText(valueField.getText().trim());
+            eValue = Double.valueOf(valueField.getText());
+
+            dVal = Math.log(eValue) / Math
+                    .log(((LogarithmicParameter) parameter).getBase())
+                    * 1000000;
+
+            if (validator.getMin() != null
+                    && validator.getMin().doubleValue() > dVal)
+            {
+              dVal = validator.getMin().doubleValue();
+              // TODO: provide visual indication that hard limit was reached for
+              // this parameter
+              // update value field to reflect any bound checking we performed.
+              valueField.setText("" + formatDouble(eValue));
+            }
+            if (validator.getMax() != null
+                    && validator.getMax().doubleValue() < dVal)
+            {
+              dVal = validator.getMax().doubleValue();
+              // TODO: provide visual indication that hard limit was reached for
+              // this parameter
+              // update value field to reflect any bound checking we performed.
+              valueField.setText("" + formatDouble(eValue));
+            }
+          } catch (Exception e)
+          {
+          }
+          ;
+          if (validator.getMin() != null && validator.getMax() != null)
+          {
+            slider.getModel().setRangeProperties((int) (dVal), 1,
+                    (int) (validator.getMin().doubleValue()),
+                    1 + (int) (validator.getMax().doubleValue()),
+                    true);
+          }
+          else
+          {
+            slider.setVisible(false);
+          }
+          return new double[] { dVal };
+        }
         else
         {
           fVal = 0f;
@@ -801,9 +889,9 @@ public class OptsAndParamsPage
 
   URL linkImageURL = getClass().getResource("/images/link.gif");
 
-  Map<String, OptionBox> optSet = new java.util.LinkedHashMap<String, OptionBox>();
+  Map<String, OptionBox> optSet = new java.util.LinkedHashMap<>();
 
-  Map<String, ParamBox> paramSet = new java.util.LinkedHashMap<String, ParamBox>();
+  Map<String, ParamBox> paramSet = new java.util.LinkedHashMap<>();
 
   public Map<String, OptionBox> getOptSet()
   {
@@ -904,7 +992,7 @@ public class OptsAndParamsPage
    */
   public List<ArgumentI> getCurrentSettings()
   {
-    List<ArgumentI> argSet = new ArrayList<ArgumentI>();
+    List<ArgumentI> argSet = new ArrayList<>();
     for (OptionBox opts : getOptSet().values())
     {
       OptionI opt = opts.getOptionIfEnabled();
diff --git a/src/jalview/gui/OverviewCanvas.java b/src/jalview/gui/OverviewCanvas.java
index 2991889..7994bf2 100644
--- a/src/jalview/gui/OverviewCanvas.java
+++ b/src/jalview/gui/OverviewCanvas.java
@@ -161,7 +161,6 @@ public class OverviewCanvas extends JComponent
               od.getColumns(av.getAlignment()));
       mg.translate(0, -od.getSequencesHeight());
     }
-    System.gc();
 
     or.removePropertyChangeListener(progressPanel);
     or = null;
@@ -183,7 +182,7 @@ public class OverviewCanvas extends JComponent
   @Override
   public void paintComponent(Graphics g)
   {
-    // super.paintComponent(g);
+    super.paintComponent(g);
 
     if (restart)
     {
diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 43b4310..ffedede 100755
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.api.AlignViewportI;
 import jalview.bin.Cache;
 import jalview.renderer.OverviewRenderer;
 import jalview.util.MessageManager;
@@ -62,7 +63,7 @@ public class OverviewPanel extends JPanel
 
   private OverviewCanvas oviewCanvas;
 
-  private AlignViewport av;
+  private AlignViewportI av;
 
   private AlignmentPanel ap;
 
@@ -170,15 +171,20 @@ public class OverviewPanel extends JPanel
       @Override
       public void mouseMoved(MouseEvent evt)
       {
-        if (od.isPositionInBox(evt.getX(), evt.getY()))
+        if (!draggingBox)
+        // don't bother changing the cursor if we're dragging the box
+        // as we can't have moved inside or out of the box in that case
         {
-          // display drag cursor at mouse position
-          setCursor(Cursor.getPredefinedCursor(Cursor.MOVE_CURSOR));
-        }
-        else
-        {
-          // reset cursor
-          setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
+          if (od.isPositionInBox(evt.getX(), evt.getY()))
+          {
+            // display drag cursor at mouse position
+            setCursor(Cursor.getPredefinedCursor(Cursor.MOVE_CURSOR));
+          }
+          else
+          {
+            // reset cursor
+            setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
+          }
         }
       }
     });
@@ -203,6 +209,10 @@ public class OverviewPanel extends JPanel
           if (!od.isPositionInBox(evt.getX(), evt.getY()))
           {
             draggingBox = false;
+
+            // display drag cursor at mouse position
+            setCursor(Cursor.getPredefinedCursor(Cursor.MOVE_CURSOR));
+
             od.updateViewportFromMouse(evt.getX(), evt.getY(),
                     av.getAlignment().getHiddenSequences(),
                     av.getAlignment().getHiddenColumns());
@@ -225,6 +235,13 @@ public class OverviewPanel extends JPanel
           showPopupMenu(evt);
         }
       }
+
+      @Override
+      public void mouseReleased(MouseEvent evt)
+      {
+        draggingBox = false;
+      }
+
     });
   }
 
diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index d081794..e736a11 100755
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -21,13 +21,13 @@
 package jalview.gui;
 
 import jalview.analysis.AlignSeq;
+import jalview.api.AlignViewportI;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.jbgui.GPairwiseAlignPanel;
 import jalview.util.MessageManager;
-import jalview.viewmodel.AlignmentViewport;
 
 import java.awt.event.ActionEvent;
 import java.util.Vector;
@@ -43,7 +43,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
 
   private static final String DASHES = "---------------------\n";
 
-  AlignmentViewport av;
+  AlignViewportI av;
 
   Vector<SequenceI> sequences;
 
@@ -51,14 +51,13 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
    * Creates a new PairwiseAlignPanel object.
    * 
    * @param viewport
-   *          DOCUMENT ME!
    */
-  public PairwiseAlignPanel(AlignmentViewport viewport)
+  public PairwiseAlignPanel(AlignViewportI viewport)
   {
     super();
     this.av = viewport;
 
-    sequences = new Vector<SequenceI>();
+    sequences = new Vector<>();
 
     SequenceGroup selectionGroup = viewport.getSelectionGroup();
     boolean isSelection = selectionGroup != null
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 0cf7ef4..e3becf6 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -158,6 +158,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
 
   JMenuItem sequenceFeature = new JMenuItem();
 
+
   JMenuItem textColour = new JMenuItem();
 
   JMenu jMenu1 = new JMenu();
@@ -233,8 +234,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
      * currently selected sequence (if there is one):
      */
     final List<SequenceI> selectedSequence = (seq == null
-            ? Collections.<SequenceI> emptyList()
-            : Arrays.asList(seq));
+            ? Collections.<SequenceI> emptyList() : Arrays.asList(seq));
+
     buildAnnotationTypesMenus(seqShowAnnotationsMenu,
             seqHideAnnotationsMenu, selectedSequence);
     configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
@@ -359,6 +360,21 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       });
       add(menuItem);
 
+      if (sequence.isHMMConsensusSequence())
+      {
+        JMenuItem selectHMM = new JCheckBoxMenuItem();
+        selectHMM.setText(MessageManager.getString("label.select_hmm"));
+        selectHMM.addActionListener(new ActionListener()
+        {
+          @Override
+          public void actionPerformed(ActionEvent e)
+          {
+            selectHMM_actionPerformed(sequence);
+          }
+        });
+        add(selectHMM);
+      }
+
       if (alignPanel.av.getSelectionGroup() != null
               && alignPanel.av.getSelectionGroup().getSize() > 1)
       {
@@ -461,7 +477,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         buildGroupURLMenu(sg, groupLinks);
       }
       // Add a 'show all structures' for the current selection
-      Hashtable<String, PDBEntry> pdbe = new Hashtable<>(), reppdb = new Hashtable<>();
+      Hashtable<String, PDBEntry> pdbe = new Hashtable<>();
+      Hashtable<String, PDBEntry> reppdb = new Hashtable<>();
 
       SequenceI sqass = null;
       for (SequenceI sq : alignPanel.av.getSequenceSelection())
@@ -1351,6 +1368,15 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
     jMenu1.add(displayNonconserved);
   }
 
+  protected void selectHMM_actionPerformed(SequenceI seq)
+  {
+    // TODO move this to Viewport
+    if (seq.isHMMConsensusSequence())
+    {
+      ap.alignFrame.setSelectedHMMSequence(seq);
+    }
+  }
+
   /**
    * Constructs the entries for the colour menu
    */
@@ -1561,15 +1587,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
 
   protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
   {
-
-    HiddenColumns hidden = new HiddenColumns();
-    BitSet inserts = new BitSet(), mask = new BitSet();
-
-    // set mask to preserve existing hidden columns outside selected group
-    if (ap.av.hasHiddenColumns())
-    {
-      ap.av.getAlignment().getHiddenColumns().markHiddenRegions(mask);
-    }
+    HiddenColumns hidden = ap.av.getAlignment().getHiddenColumns();
+    BitSet inserts = new BitSet();
 
     boolean markedPopup = false;
     // mark inserts in current selection
@@ -1577,10 +1596,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
     {
       // mark just the columns in the selection group to be hidden
       inserts.set(ap.av.getSelectionGroup().getStartRes(),
-              ap.av.getSelectionGroup().getEndRes() + 1);
-
-      // and clear that part of the mask
-      mask.andNot(inserts);
+              ap.av.getSelectionGroup().getEndRes() + 1); // TODO why +1?
 
       // now clear columns without gaps
       for (SequenceI sq : ap.av.getSelectionGroup().getSequences())
@@ -1591,29 +1607,18 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
         }
         inserts.and(sq.getInsertionsAsBits());
       }
-    }
-    else
-    {
-      // initially, mark all columns to be hidden
-      inserts.set(0, ap.av.getAlignment().getWidth());
-
-      // and clear out old hidden regions completely
-      mask.clear();
+      hidden.clearAndHideColumns(inserts, ap.av.getSelectionGroup().getStartRes(),
+              ap.av.getSelectionGroup().getEndRes());
     }
 
     // now mark for sequence under popup if we haven't already done it
-    if (!markedPopup && sequence != null)
+    else if (!markedPopup && sequence != null)
     {
-      inserts.and(sequence.getInsertionsAsBits());
-    }
+      inserts.or(sequence.getInsertionsAsBits());
 
-    // finally, preserve hidden regions outside selection
-    inserts.or(mask);
-
-    // and set hidden columns accordingly
-    hidden.hideMarkedBits(inserts);
-
-    ap.av.getAlignment().setHiddenColumns(hidden);
+      // and set hidden columns accordingly
+      hidden.hideColumns(inserts);
+    }
     refresh();
   }
 
diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index aa8369a..df35b5e 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -24,6 +24,7 @@ import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.bin.Cache;
 import jalview.gui.Help.HelpId;
 import jalview.gui.StructureViewer.ViewerType;
+import jalview.hmmer.HmmerCommand;
 import jalview.io.FileFormatI;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
@@ -48,6 +49,8 @@ import java.awt.Dimension;
 import java.awt.Font;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
+import java.awt.event.FocusAdapter;
+import java.awt.event.FocusEvent;
 import java.awt.event.MouseEvent;
 import java.io.File;
 import java.util.ArrayList;
@@ -102,6 +105,12 @@ public class Preferences extends GPreferences
   public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
 
   public static final String CHIMERA_PATH = "CHIMERA_PATH";
+  
+  public static final String HMMER_PATH = "HMMER_PATH";
+
+  public static final String HMMSEARCH_DB_PATHS = "HMMSEARCH_DB_PATHS";
+
+  public static final String HMMSEARCH_DBS = "HMMSEARCH_DBS";
 
   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
 
@@ -207,6 +216,38 @@ public class Preferences extends GPreferences
     frame.setMinimumSize(new Dimension(width, height));
 
     /*
+     * Set HMMER tab defaults
+     */
+    hmmrTrimTermini.setSelected(Cache.getDefault("TRIM_TERMINI", false));
+    if (Cache.getDefault("USE_UNIPROT", false))
+    {
+      hmmerBackgroundUniprot.setSelected(true);
+    }
+    else
+    {
+      hmmerBackgroundAlignment.setSelected(true);
+    }
+    hmmerSequenceCount
+            .setText(Cache.getProperty("SEQUENCES_TO_KEEP"));
+    hmmerPath.setText(Cache.getProperty(HMMER_PATH));
+    hmmerPath.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        validateHMMERPath(true);
+      }
+    });
+    hmmerPath.addFocusListener(new FocusAdapter()
+    {
+      @Override
+      public void focusLost(FocusEvent e)
+      {
+        validateHMMERPath(true);
+      }
+    });
+
+    /*
      * Set Visual tab defaults
      */
     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
@@ -229,6 +270,9 @@ public class Preferences extends GPreferences
             Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true));
     showConsensLogo
             .setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO", false));
+    showInformationHistogram.setSelected(
+            Cache.getDefault("SHOW_INFORMATION_HISTOGRAM", true));
+    showHMMLogo.setSelected(Cache.getDefault("SHOW_HMM_LOGO", false));
     showNpTooltip
             .setSelected(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
     showDbRefTooltip
@@ -525,7 +569,7 @@ public class Preferences extends GPreferences
     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
     userIdWidth.setEnabled(!autoIdWidth.isSelected());
     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
-    Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
+    Integer wi = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
     userIdWidth.setText(wi == null ? "" : wi.toString());
     // TODO: refactor to use common enum via FormatAdapter and allow extension
     // for new flat file formats
@@ -610,6 +654,10 @@ public class Preferences extends GPreferences
             Boolean.toString(showConsensHistogram.isSelected()));
     Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
             Boolean.toString(showConsensLogo.isSelected()));
+    Cache.applicationProperties.setProperty("SHOW_INFORMATION_HISTOGRAM",
+            Boolean.toString(showConsensHistogram.isSelected()));
+    Cache.applicationProperties.setProperty("SHOW_HMM_LOGO",
+            Boolean.toString(showHMMLogo.isSelected()));
     Cache.applicationProperties.setProperty("ANTI_ALIAS",
             Boolean.toString(smoothFont.isSelected()));
     Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
@@ -656,6 +704,39 @@ public class Preferences extends GPreferences
             maxColour.getBackground());
 
     /*
+     * Save HMMER settings
+     */
+    Cache.applicationProperties.setProperty("TRIM_TERMINI",
+            Boolean.toString(hmmrTrimTermini.isSelected()));
+    Cache.applicationProperties.setProperty("USE_UNIPROT",
+            Boolean.toString(hmmerBackgroundUniprot.isSelected()));
+    Cache.applicationProperties.setProperty("SEQUENCES_TO_KEEP",
+            hmmerSequenceCount.getText());
+    Cache.applicationProperties.setProperty(HMMER_PATH,
+            hmmerPath.getText());
+    AlignFrame[] frames = Desktop.getAlignFrames();
+    if (frames != null && frames.length > 0)
+    {
+      for (AlignFrame f : frames)
+      {
+        f.updateHMMERStatus();
+      }
+    }
+    
+    hmmrTrimTermini.setSelected(Cache.getDefault("TRIM_TERMINI", false));
+    if (Cache.getDefault("USE_UNIPROT", false))
+    {
+      hmmerBackgroundUniprot.setSelected(true);
+    }
+    else
+    {
+      hmmerBackgroundAlignment.setSelected(true);
+    }
+    hmmerSequenceCount
+            .setText(Cache.getProperty("SEQUENCES_TO_KEEP"));
+    hmmerPath.setText(Cache.getProperty(HMMER_PATH));
+
+    /*
      * Save Overview settings
      */
     Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
@@ -784,7 +865,7 @@ public class Preferences extends GPreferences
     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
             Boolean.toString(autoIdWidth.isSelected()));
     userIdWidth_actionPerformed();
-    Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
+    Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
             userIdWidth.getText());
 
     /*
@@ -898,6 +979,8 @@ public class Preferences extends GPreferences
             && (identity.isSelected() || showGroupConsensus.isSelected()));
     showConsensLogo.setEnabled(annotations.isSelected()
             && (identity.isSelected() || showGroupConsensus.isSelected()));
+    showInformationHistogram.setEnabled(annotations.isSelected());
+    showHMMLogo.setEnabled(annotations.isSelected());
   }
 
   @Override
@@ -1179,6 +1262,53 @@ public class Preferences extends GPreferences
     }
     return true;
   }
+  
+  /**
+   * Returns true if hmmer path is to a folder that contains an executable
+   * hmmbuild or hmmbuild.exe, else false (optionally after showing a warning
+   * dialog)
+   */
+  @Override
+  protected boolean validateHMMERPath(boolean showWarning)
+  {
+    String folder = hmmerPath.getText().trim();
+
+    if (HmmerCommand.getExecutable(HmmerCommand.HMMBUILD, folder) != null)
+    {
+      return true;
+    }
+    if (showWarning && folder.length() > 0)
+    {
+      JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+              MessageManager.getString("label.hmmbuild_not_found"),
+              MessageManager.getString("label.invalid_folder"),
+              JvOptionPane.ERROR_MESSAGE);
+    }
+    return false;
+  }
+
+  /**
+   * Checks if a file can be executed
+   * 
+   * @param path
+   *          the path to the file
+   * @return
+   */
+  public boolean canExecute(String path)
+  {
+    File file = new File(path);
+    if (!file.canExecute())
+    {
+      file = new File(path + ".exe");
+      {
+        if (!file.canExecute())
+        {
+          return false;
+        }
+      }
+    }
+    return true;
+  }
 
   /**
    * If Chimera is selected, check it can be found on default or user-specified
diff --git a/src/jalview/gui/RotatableCanvas.java b/src/jalview/gui/RotatableCanvas.java
index 4ef18d4..02368df 100755
--- a/src/jalview/gui/RotatableCanvas.java
+++ b/src/jalview/gui/RotatableCanvas.java
@@ -128,7 +128,6 @@ public class RotatableCanvas extends JPanel implements MouseListener,
 
   boolean applyToAllViews = false;
 
-  // Controller controller;
   public RotatableCanvas(AlignmentPanel ap)
   {
     this.av = ap.av;
@@ -136,16 +135,23 @@ public class RotatableCanvas extends JPanel implements MouseListener,
 
     addMouseWheelListener(new MouseWheelListener()
     {
+      @Override
       public void mouseWheelMoved(MouseWheelEvent e)
       {
-        if (e.getWheelRotation() > 0)
+        double wheelRotation = e.getPreciseWheelRotation();
+        if (wheelRotation > 0)
         {
+          /*
+           * zoom in
+           */
           scale = (float) (scale * 1.1);
           repaint();
         }
-
-        else
+        else if (wheelRotation < 0)
         {
+          /*
+           * zoom out
+           */
           scale = (float) (scale * 0.9);
           repaint();
         }
@@ -162,6 +168,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
 
   boolean first = true;
 
+  @Override
   public void setPoints(Vector points, int npoint)
   {
     this.points = points;
@@ -327,7 +334,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
       dim = height;
     }
 
-    return (float) ((dim * scalefactor) / (2 * maxwidth));
+    return (dim * scalefactor) / (2 * maxwidth);
   }
 
   /**
@@ -352,6 +359,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public Dimension getPreferredSize()
   {
     if (prefsize != null)
@@ -369,6 +377,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public Dimension getMinimumSize()
   {
     return getPreferredSize();
@@ -380,6 +389,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
    * @param g
    *          DOCUMENT ME!
    */
+  @Override
   public void paintComponent(Graphics g1)
   {
 
@@ -475,8 +485,8 @@ public class RotatableCanvas extends JPanel implements MouseListener,
     for (int i = 0; i < npoint; i++)
     {
       SequencePoint sp = (SequencePoint) points.elementAt(i);
-      int x = (int) ((float) (sp.coord[0] - centre[0]) * scale) + halfwidth;
-      int y = (int) ((float) (sp.coord[1] - centre[1]) * scale)
+      int x = (int) ((sp.coord[0] - centre[0]) * scale) + halfwidth;
+      int y = (int) ((sp.coord[1] - centre[1]) * scale)
               + halfheight;
       float z = sp.coord[1] - centre[2];
 
@@ -547,6 +557,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
    * @param evt
    *          DOCUMENT ME!
    */
+  @Override
   public void keyTyped(KeyEvent evt)
   {
   }
@@ -557,6 +568,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
    * @param evt
    *          DOCUMENT ME!
    */
+  @Override
   public void keyReleased(KeyEvent evt)
   {
   }
@@ -567,6 +579,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
    * @param evt
    *          DOCUMENT ME!
    */
+  @Override
   public void keyPressed(KeyEvent evt)
   {
     if (evt.getKeyCode() == KeyEvent.VK_UP)
@@ -598,6 +611,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
    * @param evt
    *          DOCUMENT ME!
    */
+  @Override
   public void mouseClicked(MouseEvent evt)
   {
   }
@@ -608,6 +622,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
    * @param evt
    *          DOCUMENT ME!
    */
+  @Override
   public void mouseEntered(MouseEvent evt)
   {
   }
@@ -618,6 +633,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
    * @param evt
    *          DOCUMENT ME!
    */
+  @Override
   public void mouseExited(MouseEvent evt)
   {
   }
@@ -628,6 +644,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
    * @param evt
    *          DOCUMENT ME!
    */
+  @Override
   public void mouseReleased(MouseEvent evt)
   {
   }
@@ -638,6 +655,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
    * @param evt
    *          DOCUMENT ME!
    */
+  @Override
   public void mousePressed(MouseEvent evt)
   {
     int x = evt.getX();
@@ -690,6 +708,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
   // controller.handleSequenceSelectionEvent(new
   // SequenceSelectionEvent(this,sel));
   // }
+  @Override
   public void mouseMoved(MouseEvent evt)
   {
     SequenceI found = findPoint(evt.getX(), evt.getY());
@@ -710,6 +729,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
    * @param evt
    *          DOCUMENT ME!
    */
+  @Override
   public void mouseDragged(MouseEvent evt)
   {
     mx = evt.getX();
@@ -725,8 +745,8 @@ public class RotatableCanvas extends JPanel implements MouseListener,
     {
       rotmat.setIdentity();
 
-      rotmat.rotate((float) (my - omy), 'x');
-      rotmat.rotate((float) (mx - omx), 'y');
+      rotmat.rotate(my - omy, 'x');
+      rotmat.rotate(mx - omx, 'y');
 
       for (int i = 0; i < npoint; i++)
       {
@@ -774,9 +794,9 @@ public class RotatableCanvas extends JPanel implements MouseListener,
     {
       SequencePoint sp = (SequencePoint) points.elementAt(i);
       int tmp1 = (int) (((sp.coord[0] - centre[0]) * scale)
-              + ((float) getWidth() / 2.0));
+              + (getWidth() / 2.0));
       int tmp2 = (int) (((sp.coord[1] - centre[1]) * scale)
-              + ((float) getHeight() / 2.0));
+              + (getHeight() / 2.0));
 
       if ((tmp1 > x1) && (tmp1 < x2) && (tmp2 > y1) && (tmp2 < y2))
       {
@@ -816,9 +836,9 @@ public class RotatableCanvas extends JPanel implements MouseListener,
     for (int i = 0; i < npoint; i++)
     {
       SequencePoint sp = (SequencePoint) points.elementAt(i);
-      int px = (int) ((float) (sp.coord[0] - centre[0]) * scale)
+      int px = (int) ((sp.coord[0] - centre[0]) * scale)
               + halfwidth;
-      int py = (int) ((float) (sp.coord[1] - centre[1]) * scale)
+      int py = (int) ((sp.coord[1] - centre[1]) * scale)
               + halfheight;
 
       if ((Math.abs(px - x) < 3) && (Math.abs(py - y) < 3))
diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index 798c833..e6bba02 100755
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -42,6 +42,7 @@ import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
 import java.beans.PropertyChangeEvent;
+import java.util.Iterator;
 import java.util.List;
 
 import javax.swing.JMenuItem;
@@ -112,7 +113,7 @@ public class ScalePanel extends JPanel
 
     if (av.hasHiddenColumns())
     {
-      x = av.getAlignment().getHiddenColumns().adjustForHiddenColumns(x);
+      x = av.getAlignment().getHiddenColumns().visibleToAbsoluteColumn(x);
     }
 
     if (x >= av.getAlignment().getWidth())
@@ -174,7 +175,7 @@ public class ScalePanel extends JPanel
       });
       pop.add(item);
 
-      if (av.getAlignment().getHiddenColumns().hasHiddenColumns())
+      if (av.getAlignment().getHiddenColumns().hasMultiHiddenColumnRegions())
       {
         item = new JMenuItem(MessageManager.getString("action.reveal_all"));
         item.addActionListener(new ActionListener()
@@ -281,7 +282,7 @@ public class ScalePanel extends JPanel
     if (av.hasHiddenColumns())
     {
       res = av.getAlignment().getHiddenColumns()
-              .adjustForHiddenColumns(res);
+              .visibleToAbsoluteColumn(res);
     }
 
     if (res >= av.getAlignment().getWidth())
@@ -336,7 +337,7 @@ public class ScalePanel extends JPanel
     int res = (evt.getX() / av.getCharWidth())
             + av.getRanges().getStartRes();
     res = Math.max(0, res);
-    res = hidden.adjustForHiddenColumns(res);
+    res = hidden.visibleToAbsoluteColumn(res);
     res = Math.min(res, av.getAlignment().getWidth() - 1);
     min = Math.min(res, min);
     max = Math.max(res, max);
@@ -392,7 +393,7 @@ public class ScalePanel extends JPanel
     reveal = av.getAlignment().getHiddenColumns()
             .getRegionWithEdgeAtRes(res);
 
-    res = av.getAlignment().getHiddenColumns().adjustForHiddenColumns(res);
+    res = av.getAlignment().getHiddenColumns().visibleToAbsoluteColumn(res);
 
     ToolTipManager.sharedInstance().registerComponent(this);
     this.setToolTipText(
@@ -409,6 +410,8 @@ public class ScalePanel extends JPanel
   @Override
   public void paintComponent(Graphics g)
   {
+    super.paintComponent(g);
+
     /*
      * shouldn't get called in wrapped mode as the scale above is
      * drawn instead by SeqCanvas.drawNorthScale
@@ -457,7 +460,7 @@ public class ScalePanel extends JPanel
         {
           if (hidden.isVisible(sel))
           {
-            sel = hidden.findColumnPosition(sel);
+            sel = hidden.absoluteToVisibleColumn(sel);
           }
           else
           {
@@ -487,23 +490,18 @@ public class ScalePanel extends JPanel
 
       if (av.getShowHiddenMarkers())
       {
-        List<Integer> positions = hidden.findHiddenRegionPositions();
-        for (int pos : positions)
+        Iterator<Integer> it = hidden.getStartRegionIterator(startx,
+                startx + widthx + 1);
+        while (it.hasNext())
         {
-          res = pos - startx;
-
-          if (res < 0 || res > widthx)
-          {
-            continue;
-          }
+          res = it.next() - startx;
 
           gg.fillPolygon(
                   new int[]
-                  { -1 + res * avCharWidth - avCharHeight / 4,
-                      -1 + res * avCharWidth + avCharHeight / 4,
-                      -1 + res * avCharWidth },
-                  new int[]
-                  { y, y, y + 2 * yOf }, 3);
+          { -1 + res * avCharWidth - avCharHeight / 4,
+              -1 + res * avCharWidth + avCharHeight / 4,
+              -1 + res * avCharWidth }, new int[]
+          { y, y, y + 2 * yOf }, 3);
         }
       }
     }
@@ -554,7 +552,11 @@ public class ScalePanel extends JPanel
             || evt.getPropertyName().equals(ViewportRanges.MOVE_VIEWPORT))
     {
       // scroll event, repaint panel
-      repaint();
+    	
+  	// Call repaint on alignment panel so that repaints from other alignment
+    // panel components can be aggregated. Otherwise performance of the overview
+    // window and others may be adversely affected.
+      av.getAlignPanel().repaint();
     }
   }
 
diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 1e1105f..2d8eb7d 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -25,6 +25,7 @@ import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.VisibleContigsIterator;
 import jalview.renderer.ScaleRenderer;
 import jalview.renderer.ScaleRenderer.ScaleMark;
 import jalview.util.Comparison;
@@ -42,6 +43,7 @@ import java.awt.RenderingHints;
 import java.awt.Shape;
 import java.awt.image.BufferedImage;
 import java.beans.PropertyChangeEvent;
+import java.util.Iterator;
 import java.util.List;
 
 import javax.swing.JComponent;
@@ -198,8 +200,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     if (av.hasHiddenColumns())
     {
       HiddenColumns hiddenColumns = av.getAlignment().getHiddenColumns();
-      startX = hiddenColumns.adjustForHiddenColumns(startx);
-      endX = hiddenColumns.adjustForHiddenColumns(endx);
+      startX = hiddenColumns.visibleToAbsoluteColumn(startx);
+      endX = hiddenColumns.visibleToAbsoluteColumn(endx);
     }
     FontMetrics fm = getFontMetrics(av.getFont());
 
@@ -295,7 +297,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
       int endSeq = ranges.getEndSeq();
       int transX = 0;
       int transY = 0;
-
+      
       gg.copyArea(horizontal * charWidth, vertical * charHeight,
               img.getWidth(), img.getHeight(), -horizontal * charWidth,
               -vertical * charHeight);
@@ -337,7 +339,10 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
       drawPanel(gg, startRes, endRes, startSeq, endSeq, 0);
       gg.translate(-transX, -transY);
 
-      repaint();
+      // Call repaint on alignment panel so that repaints from other alignment
+      // panel components can be aggregated. Otherwise performance of the
+      // overview window and others may be adversely affected.
+      av.getAlignPanel().repaint();
     } finally
     {
       fastpainting = false;
@@ -351,20 +356,20 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     
     int charHeight = av.getCharHeight();
     int charWidth = av.getCharWidth();
-
+    
     ViewportRanges ranges = av.getRanges();
-
+    
     int width = getWidth();
     int height = getHeight();
-
+    
     width -= (width % charWidth);
     height -= (height % charHeight);
-
+    
     // selectImage is the selection group outline image
     BufferedImage selectImage = drawSelectionGroup(
             ranges.getStartRes(), ranges.getEndRes(),
             ranges.getStartSeq(), ranges.getEndSeq());
-
+    
     if ((img != null) && (fastPaint
             || (getVisibleRect().width != g.getClipBounds().width)
             || (getVisibleRect().height != g.getClipBounds().height)))
@@ -388,16 +393,16 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
         gg = (Graphics2D) img.getGraphics();
         gg.setFont(av.getFont());
       }
-
+    
       if (av.antiAlias)
       {
         gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
                 RenderingHints.VALUE_ANTIALIAS_ON);
       }
-
+    
       gg.setColor(Color.white);
       gg.fillRect(0, 0, img.getWidth(), img.getHeight());
-
+    
       if (av.getWrapAlignment())
       {
         drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes());
@@ -407,7 +412,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
         drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(),
                 ranges.getStartSeq(), ranges.getEndSeq(), 0);
       }
-
+    
       // lcimg is a local *copy* of img which we'll draw selectImage on top of
       BufferedImage lcimg = buildLocalImage(selectImage);
       g.drawImage(lcimg, 0, 0, this);
@@ -504,8 +509,11 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
   private BufferedImage buildLocalImage(BufferedImage selectImage)
   {
     // clone the cached image
-    BufferedImage lcimg = new BufferedImage(img.getWidth(), img.getHeight(),
-            img.getType());
+	  BufferedImage lcimg = new BufferedImage(img.getWidth(), img.getHeight(),
+	            img.getType());
+
+    // BufferedImage lcimg = new BufferedImage(img.getWidth(), img.getHeight(),
+    // img.getType());
     Graphics2D g2d = lcimg.createGraphics();
     g2d.drawImage(img, 0, 0, null);
 
@@ -545,8 +553,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
 
     try
     {
-      lcimg = new BufferedImage(width, height,
-              BufferedImage.TYPE_INT_ARGB); // ARGB so alpha compositing works
+    	lcimg = new BufferedImage(width, height,
+                BufferedImage.TYPE_INT_ARGB); // ARGB so alpha compositing works
     } catch (OutOfMemoryError er)
     {
       System.gc();
@@ -890,11 +898,14 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     int charWidth = av.getCharWidth();
 
     g.setColor(Color.blue);
+    int res;
     HiddenColumns hidden = av.getAlignment().getHiddenColumns();
-    List<Integer> positions = hidden.findHiddenRegionPositions();
-    for (int pos : positions)
+
+    Iterator<Integer> it = hidden.getStartRegionIterator(startColumn,
+            endColumn);
+    while (it.hasNext())
     {
-      int res = pos - startColumn;
+      res = it.next() - startColumn;
 
       if (res < 0 || res > endColumn - startColumn + 1)
       {
@@ -943,7 +954,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     if (av.hasHiddenColumns())
     {
       maxwidth = av.getAlignment().getHiddenColumns()
-              .findColumnPosition(maxwidth);
+              .absoluteToVisibleColumn(maxwidth);
     }
 
     // chop the wrapped alignment extent up into panel-sized blocks and treat
@@ -1021,29 +1032,23 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     else
     {
       int screenY = 0;
-      final int screenYMax = endRes - startRes;
-      int blockStart = startRes;
-      int blockEnd = endRes;
+      int blockStart;
+      int blockEnd;
 
-      for (int[] region : av.getAlignment().getHiddenColumns()
-              .getHiddenColumnsCopy())
-      {
-        int hideStart = region[0];
-        int hideEnd = region[1];
+      HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+      VisibleContigsIterator regions = hidden
+              .getVisContigsIterator(startRes, endRes + 1, true);
 
-        if (hideStart <= blockStart)
-        {
-          blockStart += (hideEnd - hideStart) + 1;
-          continue;
-        }
+      while (regions.hasNext())
+      {
+        int[] region = regions.next();
+        blockEnd = region[1];
+        blockStart = region[0];
 
         /*
          * draw up to just before the next hidden region, or the end of
          * the visible region, whichever comes first
          */
-        blockEnd = Math.min(hideStart - 1, blockStart + screenYMax
-                - screenY);
-
         g1.translate(screenY * charWidth, 0);
 
         draw(g1, blockStart, blockEnd, startSeq, endSeq, yOffset);
@@ -1052,7 +1057,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
          * draw the downline of the hidden column marker (ScalePanel draws the
          * triangle on top) if we reached it
          */
-        if (av.getShowHiddenMarkers() && blockEnd == hideStart - 1)
+        if (av.getShowHiddenMarkers()
+                && (regions.hasNext() || regions.endsAtHidden()))
         {
           g1.setColor(Color.blue);
 
@@ -1063,23 +1069,6 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
 
         g1.translate(-screenY * charWidth, 0);
         screenY += blockEnd - blockStart + 1;
-        blockStart = hideEnd + 1;
-
-        if (screenY > screenYMax)
-        {
-          // already rendered last block
-          return;
-        }
-      }
-
-      if (screenY <= screenYMax)
-      {
-        // remaining visible region to render
-        blockEnd = blockStart + screenYMax - screenY;
-        g1.translate(screenY * charWidth, 0);
-        draw(g1, blockStart, blockEnd, startSeq, endSeq, yOffset);
-
-        g1.translate(-screenY * charWidth, 0);
       }
     }
 
@@ -1137,16 +1126,16 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
       if (av.hasSearchResults())
       {
         SearchResultsI searchResults = av.getSearchResults();
-        int[] visibleResults = searchResults.getResults(nextSeq,
-                startRes, endRes);
+        int[] visibleResults = searchResults.getResults(nextSeq, startRes,
+                endRes);
         if (visibleResults != null)
         {
           for (int r = 0; r < visibleResults.length; r += 2)
           {
             seqRdr.drawHighlightedText(nextSeq, visibleResults[r],
-                    visibleResults[r + 1], (visibleResults[r] - startRes)
-                            * charWidth, offset
-                            + ((i - startSeq) * charHeight));
+                    visibleResults[r + 1],
+                    (visibleResults[r] - startRes) * charWidth,
+                    offset + ((i - startSeq) * charHeight));
           }
         }
       }
@@ -1278,7 +1267,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
 
       // convert the cursorX into a position on the visible alignment
       int cursor_xpos = av.getAlignment().getHiddenColumns()
-              .findColumnPosition(cursorX);
+              .absoluteToVisibleColumn(cursorX);
 
       if (av.getAlignment().getHiddenColumns().isVisible(cursorX))
       {
@@ -1377,22 +1366,17 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     {
       // package into blocks of visible columns
       int screenY = 0;
-      int blockStart = startRes;
-      int blockEnd = endRes;
+      int blockStart;
+      int blockEnd;
 
-      for (int[] region : av.getAlignment().getHiddenColumns()
-              .getHiddenColumnsCopy())
+      HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+      VisibleContigsIterator regions = hidden
+              .getVisContigsIterator(startRes, endRes + 1, true);
+      while (regions.hasNext())
       {
-        int hideStart = region[0];
-        int hideEnd = region[1];
-
-        if (hideStart <= blockStart)
-        {
-          blockStart += (hideEnd - hideStart) + 1;
-          continue;
-        }
-
-        blockEnd = hideStart - 1;
+        int[] region = regions.next();
+        blockEnd = region[1];
+        blockStart = region[0];
 
         g.translate(screenY * charWidth, 0);
         drawPartialGroupOutline(g, group,
@@ -1400,24 +1384,6 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
 
         g.translate(-screenY * charWidth, 0);
         screenY += blockEnd - blockStart + 1;
-        blockStart = hideEnd + 1;
-
-        if (screenY > (endRes - startRes))
-        {
-          // already rendered last block
-          break;
-        }
-      }
-
-      if (screenY <= (endRes - startRes))
-      {
-        // remaining visible region to render
-        blockEnd = blockStart + (endRes - startRes) - screenY;
-        g.translate(screenY * charWidth, 0);
-        drawPartialGroupOutline(g, group,
-                blockStart, blockEnd, startSeq, endSeq, offset);
-        
-        g.translate(-screenY * charWidth, 0);
       }
     }
   }
@@ -1681,9 +1647,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     if (av.hasHiddenColumns())
     {
       firstVisibleColumn = alignment.getHiddenColumns()
-              .adjustForHiddenColumns(firstVisibleColumn);
+              .visibleToAbsoluteColumn(firstVisibleColumn);
       lastVisibleColumn = alignment.getHiddenColumns()
-              .adjustForHiddenColumns(lastVisibleColumn);
+              .visibleToAbsoluteColumn(lastVisibleColumn);
     }
 
     for (int seqNo = ranges.getStartSeq(); seqNo <= ranges
@@ -1726,8 +1692,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
       if (av.hasHiddenColumns())
       {
         firstCol = alignment.getHiddenColumns()
-                .findColumnPosition(firstCol);
-        lastCol = alignment.getHiddenColumns().findColumnPosition(lastCol);
+                .absoluteToVisibleColumn(firstCol);
+        lastCol = alignment.getHiddenColumns().absoluteToVisibleColumn(lastCol);
       }
       int transX = (firstCol - ranges.getStartRes()) * av.getCharWidth();
       int transY = (firstSeq - ranges.getStartSeq()) * av.getCharHeight();
@@ -1784,14 +1750,30 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
         scrollX = -range;
       }
     }
-    // Both scrolling and resizing change viewport ranges: scrolling changes
-    // both start and end points, but resize only changes end values.
-    // Here we only want to fastpaint on a scroll, with resize using a normal
-    // paint, so scroll events are identified as changes to the horizontal or
-    // vertical start value.
-    if (eventName.equals(ViewportRanges.STARTRES))
-    {
-      if (av.getWrapAlignment())
+      // Both scrolling and resizing change viewport ranges: scrolling changes
+      // both start and end points, but resize only changes end values.
+      // Here we only want to fastpaint on a scroll, with resize using a normal
+      // paint, so scroll events are identified as changes to the horizontal or
+      // vertical start value.
+      if (eventName.equals(ViewportRanges.STARTRES))
+      {
+    	  if (av.getWrapAlignment())
+          {
+            fastPaintWrapped(scrollX);
+          }
+          else
+          {
+            fastPaint(scrollX, 0);
+          }
+      }
+      else if (eventName.equals(ViewportRanges.STARTSEQ))
+      {
+        // scroll
+        fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue());
+      }
+      else if (eventName.equals(ViewportRanges.STARTRESANDSEQ))
+      {
+        if (av.getWrapAlignment())
         {
           fastPaintWrapped(scrollX);
         }
@@ -1811,14 +1793,6 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
       {
         fastPaintWrapped(scrollX);
       }
-      else
-      {
-        fastPaint(scrollX, 0);
-      }
-      // bizarrely, we only need to scroll on the x value here as fastpaint
-      // copies the full height of the image anyway. Passing in the y value
-      // causes nasty repaint artefacts, which only disappear on a full
-      // repaint.
     }
   }
 
@@ -1835,9 +1809,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
   {
     ViewportRanges ranges = av.getRanges();
 
-    // if (Math.abs(scrollX) > ranges.getViewportWidth())
-    // JAL-2836, 2836 temporarily removed wrapped fastpaint for release 2.10.3
-    if (true)
+    if (Math.abs(scrollX) > ranges.getViewportWidth())
     {
       /*
        * shift of more than one view width is 
@@ -2115,9 +2087,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     if (av.hasHiddenColumns())
     {
       firstVisibleColumn = alignment.getHiddenColumns()
-              .adjustForHiddenColumns(firstVisibleColumn);
+              .visibleToAbsoluteColumn(firstVisibleColumn);
       lastVisibleColumn = alignment.getHiddenColumns()
-              .adjustForHiddenColumns(lastVisibleColumn);
+              .visibleToAbsoluteColumn(lastVisibleColumn);
     }
 
     int gapHeight = charHeight * (av.getScaleAboveWrapped() ? 2 : 1);
@@ -2156,7 +2128,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
               if (av.hasHiddenColumns())
               {
                 displayColumn = alignment.getHiddenColumns()
-                        .findColumnPosition(displayColumn);
+                        .absoluteToVisibleColumn(displayColumn);
               }
 
               /*
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index fb6efe5..193d0ee 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -246,7 +246,7 @@ public class SeqPanel extends JPanel
     if (av.hasHiddenColumns())
     {
       res = av.getAlignment().getHiddenColumns()
-              .adjustForHiddenColumns(res);
+              .visibleToAbsoluteColumn(res);
     }
 
     return res;
@@ -359,13 +359,25 @@ public class SeqPanel extends JPanel
       int original = seqCanvas.cursorX - dx;
       int maxWidth = av.getAlignment().getWidth();
 
-      // TODO: once JAL-2759 is ready, change this loop to something more
-      // efficient
-      while (!hidden.isVisible(seqCanvas.cursorX)
-              && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0
-              && dx != 0)
+      if (!hidden.isVisible(seqCanvas.cursorX))
       {
-        seqCanvas.cursorX += dx;
+        int visx = hidden.absoluteToVisibleColumn(seqCanvas.cursorX - dx);
+        int[] region = hidden.getRegionWithEdgeAtRes(visx);
+
+        if (region != null) // just in case
+        {
+          if (dx == 1)
+          {
+            // moving right
+            seqCanvas.cursorX = region[1] + 1;
+          }
+          else if (dx == -1)
+          {
+            // moving left
+            seqCanvas.cursorX = region[0] - 1;
+          }
+        }
+        seqCanvas.cursorX = (seqCanvas.cursorX < 0) ? 0 : seqCanvas.cursorX;
       }
 
       if (seqCanvas.cursorX >= maxWidth
@@ -420,7 +432,7 @@ public class SeqPanel extends JPanel
       {
         // scrollToWrappedVisible expects x-value to have hidden cols subtracted
         int x = av.getAlignment().getHiddenColumns()
-                .findColumnPosition(seqCanvas.cursorX);
+                .absoluteToVisibleColumn(seqCanvas.cursorX);
         av.getRanges().scrollToWrappedVisible(x);
       }
       else
@@ -1260,9 +1272,9 @@ public class SeqPanel extends JPanel
     {
       fixedColumns = true;
       int y1 = av.getAlignment().getHiddenColumns()
-              .getHiddenBoundaryLeft(startres);
+              .getNextHiddenBoundary(true, startres);
       int y2 = av.getAlignment().getHiddenColumns()
-              .getHiddenBoundaryRight(startres);
+              .getNextHiddenBoundary(false, startres);
 
       if ((insertGap && startres > y1 && lastres < y1)
               || (!insertGap && startres < y2 && lastres > y2))
@@ -1338,7 +1350,8 @@ public class SeqPanel extends JPanel
           if (sg.getSize() == av.getAlignment().getHeight())
           {
             if ((av.hasHiddenColumns() && startres < av.getAlignment()
-                    .getHiddenColumns().getHiddenBoundaryRight(startres)))
+                    .getHiddenColumns()
+                    .getNextHiddenBoundary(false, startres)))
             {
               endEditing();
               return;
@@ -1657,7 +1670,8 @@ public class SeqPanel extends JPanel
   public void mouseWheelMoved(MouseWheelEvent e)
   {
     e.consume();
-    if (e.getWheelRotation() > 0)
+    double wheelRotation = e.getPreciseWheelRotation();
+    if (wheelRotation > 0)
     {
       if (e.isShiftDown())
       {
@@ -1669,7 +1683,7 @@ public class SeqPanel extends JPanel
         av.getRanges().scrollUp(false);
       }
     }
-    else
+    else if (wheelRotation < 0)
     {
       if (e.isShiftDown())
       {
@@ -1853,7 +1867,7 @@ public class SeqPanel extends JPanel
 
     // always do this - annotation has own state
     // but defer colourscheme update until hidden sequences are passed in
-    boolean vischange = stretchGroup.recalcConservation(true);
+    boolean vischange = stretchGroup.recalcAnnotations(true);
     updateOverviewAndStructs |= vischange && av.isSelectionDefinedGroup()
             && afterDrag;
     if (stretchGroup.cs != null)
diff --git a/src/jalview/gui/SplitFrame.java b/src/jalview/gui/SplitFrame.java
index 5bff407..56d1fac 100644
--- a/src/jalview/gui/SplitFrame.java
+++ b/src/jalview/gui/SplitFrame.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.api.AlignViewportI;
 import jalview.api.SplitContainerI;
 import jalview.datamodel.AlignmentI;
 import jalview.jbgui.GAlignFrame;
@@ -215,8 +216,8 @@ public class SplitFrame extends GSplitFrame implements SplitContainerI
     topFrame.alignPanel.adjustAnnotationHeight();
     bottomFrame.alignPanel.adjustAnnotationHeight();
 
-    final AlignViewport topViewport = topFrame.viewport;
-    final AlignViewport bottomViewport = bottomFrame.viewport;
+    final AlignViewportI topViewport = topFrame.viewport;
+    final AlignViewportI bottomViewport = bottomFrame.viewport;
     final AlignmentI topAlignment = topViewport.getAlignment();
     final AlignmentI bottomAlignment = bottomViewport.getAlignment();
     boolean topAnnotations = topViewport.isShowAnnotation();
diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 217f653..198aa62 100644
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -21,6 +21,7 @@
 
 package jalview.gui;
 
+import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Jalview;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
@@ -53,6 +54,8 @@ import java.util.Vector;
 import javax.swing.JCheckBox;
 import javax.swing.JComboBox;
 import javax.swing.JLabel;
+import javax.swing.JTable;
+import javax.swing.SwingUtilities;
 import javax.swing.table.AbstractTableModel;
 
 /**
@@ -728,16 +731,65 @@ public class StructureChooser extends GStructureChooser
   }
 
   /**
+   * select structures for viewing by their PDB IDs
+   * 
+   * @param pdbids
+   * @return true if structures were found and marked as selected
+   */
+  public boolean selectStructure(String... pdbids)
+  {
+    boolean found = false;
+
+    FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
+            .getSelectedItem());
+    String currentView = selectedFilterOpt.getView();
+    JTable restable = (currentView == VIEWS_FILTER) ? getResultTable()
+            : (currentView == VIEWS_LOCAL_PDB) ? tbl_local_pdb : null;
+
+    if (restable == null)
+    {
+      // can't select (enter PDB ID, or load file - need to also select which
+      // sequence to associate with)
+      return false;
+    }
+
+    int pdbIdColIndex = restable.getColumn("PDB Id").getModelIndex();
+    for (int r = 0; r < restable.getRowCount(); r++)
+    {
+      for (int p = 0; p < pdbids.length; p++)
+      {
+        if (String.valueOf(restable.getValueAt(r, pdbIdColIndex))
+                .equalsIgnoreCase(pdbids[p]))
+        {
+          restable.setRowSelectionInterval(r, r);
+          found = true;
+        }
+      }
+    }
+    return found;
+  }
+  /**
    * Handles action event for btn_ok
    */
   @Override
   public void ok_ActionPerformed()
   {
+    showStructures(false);
+  }
+
+  /**
+   * structure viewer opened by this dialog, or null
+   */
+  private StructureViewer sViewer = null;
+
+  public void showStructures(boolean waitUntilFinished)
+  {
+
     final StructureSelectionManager ssm = ap.getStructureSelectionManager();
 
     final int preferredHeight = pnl_filter.getHeight();
 
-    new Thread(new Runnable()
+    Runnable viewStruc = new Runnable()
     {
       @Override
       public void run()
@@ -745,21 +797,24 @@ public class StructureChooser extends GStructureChooser
         FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
                 .getSelectedItem());
         String currentView = selectedFilterOpt.getView();
+        JTable restable = (currentView == VIEWS_FILTER) ? getResultTable()
+                : tbl_local_pdb;
+
         if (currentView == VIEWS_FILTER)
         {
-          int pdbIdColIndex = getResultTable().getColumn("PDB Id")
+          int pdbIdColIndex = restable.getColumn("PDB Id")
                   .getModelIndex();
-          int refSeqColIndex = getResultTable().getColumn("Ref Sequence")
+          int refSeqColIndex = restable.getColumn("Ref Sequence")
                   .getModelIndex();
-          int[] selectedRows = getResultTable().getSelectedRows();
+          int[] selectedRows = restable.getSelectedRows();
           PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
           int count = 0;
           List<SequenceI> selectedSeqsToView = new ArrayList<>();
           for (int row : selectedRows)
           {
-            String pdbIdStr = getResultTable()
+            String pdbIdStr = restable
                     .getValueAt(row, pdbIdColIndex).toString();
-            SequenceI selectedSeq = (SequenceI) getResultTable()
+            SequenceI selectedSeq = (SequenceI) restable
                     .getValueAt(row, refSeqColIndex);
             selectedSeqsToView.add(selectedSeq);
             PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
@@ -780,7 +835,8 @@ public class StructureChooser extends GStructureChooser
           }
           SequenceI[] selectedSeqs = selectedSeqsToView
                   .toArray(new SequenceI[selectedSeqsToView.size()]);
-          launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
+          sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
+                  selectedSeqs);
         }
         else if (currentView == VIEWS_LOCAL_PDB)
         {
@@ -803,7 +859,8 @@ public class StructureChooser extends GStructureChooser
           }
           SequenceI[] selectedSeqs = selectedSeqsToView
                   .toArray(new SequenceI[selectedSeqsToView.size()]);
-          launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
+          sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
+                  selectedSeqs);
         }
         else if (currentView == VIEWS_ENTER_ID)
         {
@@ -832,7 +889,7 @@ public class StructureChooser extends GStructureChooser
           }
 
           PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
-          launchStructureViewer(ssm, pdbEntriesToView, ap,
+          sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
                   new SequenceI[]
                   { selectedSequence });
         }
@@ -849,14 +906,40 @@ public class StructureChooser extends GStructureChooser
                           DataSourceType.FILE, selectedSequence, true,
                           Desktop.instance);
 
-          launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap,
+          sViewer = launchStructureViewer(
+                  ssm, new PDBEntry[]
+                  { fileEntry }, ap,
                   new SequenceI[]
                   { selectedSequence });
         }
-        closeAction(preferredHeight);
-        mainFrame.dispose();
+        SwingUtilities.invokeLater(new Runnable()
+        {
+          @Override
+          public void run()
+          {
+            closeAction(preferredHeight);
+            mainFrame.dispose();
+          }
+        });
       }
-    }).start();
+    };
+    Thread runner = new Thread(viewStruc);
+    runner.start();
+    if (waitUntilFinished)
+    {
+      while (sViewer == null ? runner.isAlive()
+              : (sViewer.sview == null ? true
+                      : !sViewer.sview.hasMapping()))
+      {
+        try
+        {
+          Thread.sleep(300);
+        } catch (InterruptedException ie)
+        {
+
+        }
+      }
+    }
   }
 
   private PDBEntry getFindEntry(String id, Vector<PDBEntry> pdbEntries)
@@ -874,7 +957,8 @@ public class StructureChooser extends GStructureChooser
     return foundEntry;
   }
 
-  private void launchStructureViewer(StructureSelectionManager ssm,
+  private StructureViewer launchStructureViewer(
+          StructureSelectionManager ssm,
           final PDBEntry[] pdbEntriesToView,
           final AlignmentPanel alignPanel, SequenceI[] sequences)
   {
@@ -948,6 +1032,7 @@ public class StructureChooser extends GStructureChooser
       sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
     }
     setProgressBar(null, progressId);
+    return sViewer;
   }
 
   /**
@@ -1178,4 +1263,9 @@ public class StructureChooser extends GStructureChooser
   {
     return progressBar.operationInProgress();
   }
+
+  public JalviewStructureDisplayI getOpenedStructureViewer()
+  {
+    return sViewer == null ? null : sViewer.sview;
+  }
 }
diff --git a/src/jalview/gui/StructureViewer.java b/src/jalview/gui/StructureViewer.java
index fb37b77..f37df71 100644
--- a/src/jalview/gui/StructureViewer.java
+++ b/src/jalview/gui/StructureViewer.java
@@ -104,7 +104,7 @@ public class StructureViewer
             new PDBEntry[seqsForPdbs.size()]);
     SequenceI[][] theSeqs = seqsForPdbs.values().toArray(
             new SequenceI[seqsForPdbs.size()][]);
-    JalviewStructureDisplayI sview = null;
+
     if (viewerType.equals(ViewerType.JMOL))
     {
       sview = new AppJmol(ap, pdbsForFile, theSeqs);
@@ -203,7 +203,7 @@ public class StructureViewer
   private JalviewStructureDisplayI onlyOnePdb(PDBEntry[] pdbs,
           SequenceI[] seqsForPdbs, AlignmentPanel ap)
   {
-    List<SequenceI> seqs = new ArrayList<SequenceI>();
+    List<SequenceI> seqs = new ArrayList<>();
     if (pdbs == null || pdbs.length == 0)
     {
       return null;
@@ -227,11 +227,12 @@ public class StructureViewer
             ap);
   }
 
+  JalviewStructureDisplayI sview = null;
+
   public JalviewStructureDisplayI viewStructures(PDBEntry pdb,
           SequenceI[] seqsForPdb, AlignmentPanel ap)
   {
     ViewerType viewerType = getViewerType();
-    JalviewStructureDisplayI sview = null;
     if (viewerType.equals(ViewerType.JMOL))
     {
       sview = new AppJmol(pdb, seqsForPdb, null, ap);
@@ -270,7 +271,6 @@ public class StructureViewer
     final boolean usetoColourbyseq = viewerData.isColourWithAlignPanel();
     final boolean viewerColouring = viewerData.isColourByViewer();
 
-    JalviewStructureDisplayI sview = null;
     switch (type)
     {
     case JMOL:
@@ -287,4 +287,16 @@ public class StructureViewer
     return sview;
   }
 
+  public boolean isBusy()
+  {
+    if (sview != null)
+    {
+      if (!sview.hasMapping())
+      {
+        return true;
+      }
+    }
+    return false;
+  }
+
 }
diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index 31c20ed..93d675a 100644
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -34,6 +34,7 @@ import jalview.io.JalviewFileView;
 import jalview.jbgui.GStructureViewer;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemes;
+import jalview.structure.StructureMapping;
 import jalview.structures.models.AAStructureBindingModel;
 import jalview.util.MessageManager;
 
@@ -102,9 +103,9 @@ public abstract class StructureViewerBase extends GStructureViewer
 
   protected boolean alignAddedStructures = false;
 
-  protected boolean _started = false;
+  protected volatile boolean _started = false;
 
-  protected boolean addingStructures = false;
+  protected volatile boolean addingStructures = false;
 
   protected Thread worker = null;
 
@@ -113,6 +114,13 @@ public abstract class StructureViewerBase extends GStructureViewer
   protected JMenu viewSelectionMenu;
 
   /**
+   * set after sequence colouring has been applied for this structure viewer.
+   * used to determine if the final sequence/structure mapping has been
+   * determined
+   */
+  protected volatile boolean seqColoursApplied = false;
+
+  /**
    * Default constructor
    */
   public StructureViewerBase()
@@ -909,6 +917,7 @@ public abstract class StructureViewerBase extends GStructureViewer
       {
         binding.colourBySequence(ap);
       }
+      seqColoursApplied = true;
     }
   }
 
@@ -1028,4 +1037,42 @@ public abstract class StructureViewerBase extends GStructureViewer
       seqColour_actionPerformed(null);
     }
   }
+
+  @Override
+  public boolean hasMapping()
+  {
+    if (worker != null && (addingStructures || _started))
+    {
+      return false;
+    }
+    if (getBinding() == null)
+    {
+      if (_aps == null || _aps.size() == 0)
+      {
+        // viewer has been closed, but we did at some point run.
+        return true;
+      }
+      return false;
+    }
+    String[] pdbids = getBinding().getStructureFiles();
+    if (pdbids == null)
+    {
+      return false;
+    }
+    int p=0;
+    for (String pdbid:pdbids) {
+      StructureMapping sm[] = getBinding().getSsm().getMapping(pdbid);
+      if (sm!=null && sm.length>0 && sm[0]!=null) {
+        p++;
+      }
+    }
+    // only return true if there is a mapping for every structure file we have loaded
+    if (p == 0 || p != pdbids.length)
+    {
+      return false;
+    }
+    // and that coloring has been applied
+    return seqColoursApplied;
+  }
+
 }
diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java
index d2086e0..973cfe8 100644
--- a/src/jalview/gui/VamsasApplication.java
+++ b/src/jalview/gui/VamsasApplication.java
@@ -1074,16 +1074,16 @@ public class VamsasApplication implements SelectionSource, VamsasSource
                   }
                   else
                   {
-                    // int[] intervals = colsel.getVisibleContigs(
-                    // seqsel.getStartRes(), seqsel.getEndRes() + 1);
-                    int[] intervals = hidden.getVisibleContigs(
-                            seqsel.getStartRes(), seqsel.getEndRes() + 1);
-                    for (int iv = 0; iv < intervals.length; iv += 2)
+                    Iterator<int[]> intervals = hidden
+                            .getVisContigsIterator(seqsel.getStartRes(),
+                                    seqsel.getEndRes() + 1, false);
+                    while (intervals.hasNext())
                     {
+                      int[] region = intervals.next();
                       Seg s = new Seg();
-                      s.setStart(intervals[iv] + 1); // vamsas indices begin at
-                      // 1, not zero.
-                      s.setEnd(intervals[iv + 1] + 1);
+                      s.setStart(region[0] + 1); // vamsas indices begin at 1,
+                                                 // not zero.
+                      s.setEnd(region[1] + 1);
                       s.setInclusive(true);
                       range.addSeg(s);
                     }
diff --git a/src/jalview/gui/WsJobParameters.java b/src/jalview/gui/WsJobParameters.java
index 10798f6..af52d43 100644
--- a/src/jalview/gui/WsJobParameters.java
+++ b/src/jalview/gui/WsJobParameters.java
@@ -69,14 +69,13 @@ import javax.swing.border.TitledBorder;
 import javax.swing.event.DocumentEvent;
 import javax.swing.event.DocumentListener;
 
-import net.miginfocom.swing.MigLayout;
-
 import compbio.metadata.Argument;
 import compbio.metadata.Option;
 import compbio.metadata.Parameter;
 import compbio.metadata.Preset;
 import compbio.metadata.PresetManager;
 import compbio.metadata.RunnerConfig;
+import net.miginfocom.swing.MigLayout;
 
 /**
  * job parameter editing/browsing dialog box. User can browse existing settings
@@ -159,6 +158,21 @@ public class WsJobParameters extends JPanel implements ItemListener,
     this(service, null);
   }
 
+  public WsJobParameters(JFrame parent, ParamDatastoreI store,
+          WsParamSetI preset,
+          List<ArgumentI> args)
+  {
+    super();
+    jbInit();
+    this.paramStore = store;
+    this.service = null;
+    // argSetModified(false);
+    // populate parameter table
+    init(preset, args);
+    // display in new JFrame attached to parent.
+    validate();
+  }
+
   public WsJobParameters(Jws2Instance service, WsParamSetI preset)
   {
     this(null, service, preset, null);
@@ -217,10 +231,13 @@ public class WsJobParameters extends JPanel implements ItemListener,
   {
 
     frame = new JDialog(Desktop.instance, true);
+    if (service != null)
+    {
+      frame.setTitle(MessageManager.formatMessage("label.edit_params_for",
+              new String[]
+      { service.getActionText() }));
+    }
 
-    frame.setTitle(MessageManager.formatMessage("label.edit_params_for",
-            new String[]
-            { service.getActionText() }));
     Rectangle deskr = Desktop.instance.getBounds();
     Dimension pref = this.getPreferredSize();
     frame.setBounds(
@@ -541,6 +558,12 @@ public class WsJobParameters extends JPanel implements ItemListener,
                  // null;
     }
 
+    init(p, jobArgset);
+
+  }
+
+  void init(WsParamSetI p, List<ArgumentI> jobArgset)
+  {
     Hashtable exnames = new Hashtable();
     for (int i = 0, iSize = setName.getItemCount(); i < iSize; i++)
     {
@@ -594,7 +617,6 @@ public class WsJobParameters extends JPanel implements ItemListener,
       }
     }
     settingDialog = false;
-
   }
 
   @SuppressWarnings("unchecked")
@@ -967,7 +989,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
     int p = 0;
     if (args.length > 0)
     {
-      Vector<String> services = new Vector<String>();
+      Vector<String> services = new Vector<>();
       services.addElement(args[p++]);
       Jws2Discoverer.getDiscoverer().setServiceUrls(services);
     }
@@ -1340,8 +1362,8 @@ public class WsJobParameters extends JPanel implements ItemListener,
     if (e.getSource() == setName && e.getStateChange() == e.SELECTED)
     {
       final String setname = (String) setName.getSelectedItem();
-      System.out.println("Item state changed for " + setname
-              + " (handling ? " + !settingDialog + ")");
+      // System.out.println("Item state changed for " + setname
+      // + " (handling ? " + !settingDialog + ")");
       if (settingDialog)
       {
         // ignore event
diff --git a/src/jalview/hmmer/HMMAlign.java b/src/jalview/hmmer/HMMAlign.java
new file mode 100644
index 0000000..44828aa
--- /dev/null
+++ b/src/jalview/hmmer/HMMAlign.java
@@ -0,0 +1,349 @@
+package jalview.hmmer;
+
+import jalview.analysis.AlignmentSorter;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentOrder;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.HiddenMarkovModel;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
+import jalview.gui.SplitFrame;
+import jalview.io.DataSourceType;
+import jalview.io.StockholmFile;
+import jalview.util.MessageManager;
+import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
+import jalview.ws.params.ArgumentI;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+
+import javax.swing.JInternalFrame;
+
+public class HMMAlign extends HmmerCommand
+{
+  static final String HMMALIGN = "hmmalign";
+
+  static final String ARG_TRIM = "--trim";
+
+  private final AlignmentI dataset;
+
+  /**
+   * Constructor for the HMMAlignThread
+   * 
+   * @param af
+   * @param args
+   */
+  public HMMAlign(AlignFrame af, List<ArgumentI> args)
+  {
+    super(af, args);
+    if (alignment.getDataset() != null)
+    {
+      dataset = alignment.getDataset();
+    }
+    else
+    {
+      dataset = null;
+    }
+  }
+
+  /**
+   * Runs the HMMAlignThread: the data on the alignment or group is exported,
+   * then the command is executed in the command line and then the data is
+   * imported and displayed in a new frame (if true). The command is executed
+   * for each segment of the alignment. Call this method directly to execute
+   * synchronously, or via start() in a new Thread for asynchronously.
+   */
+  @Override
+  public void run()
+  {
+    HiddenMarkovModel hmm = af.getSelectedHMM();
+    if (hmm == null)
+    {
+      System.err.println("Can't run hmmalign as no HMM profile selected");
+      return;
+    }
+
+    long msgId = System.currentTimeMillis();
+    af.setProgressBar(MessageManager.getString("status.running_hmmalign"),
+            msgId);
+
+    AlignmentView msa = af.gatherSequencesForAlignment();
+    SequenceI[][] subAlignments = msa.getVisibleContigs(alignment.getGapCharacter());
+
+    List<AlignmentOrder> allOrders = new ArrayList<>();
+
+    SequenceI[][] allResults = new SequenceI[subAlignments.length][];
+    int job = 0;
+    for (SequenceI[] seqs : subAlignments)
+    {
+      Hashtable sequencesHash = stashSequences(seqs);
+      try
+      {
+        File modelFile = createTempFile("hmm", ".hmm");
+        File alignmentFile = createTempFile("output", ".sto");
+        File resultFile = createTempFile("input", ".sto");
+
+        exportStockholm(seqs, alignmentFile.getAbsoluteFile(), null);
+        exportHmm(hmm, modelFile.getAbsoluteFile());
+
+        boolean ran = runCommand(modelFile, alignmentFile, resultFile);
+        if (!ran)
+        {
+          JvOptionPane.showInternalMessageDialog(af,
+                  MessageManager.getString("warn.hmmalign_failed"));
+          return;
+        }
+
+        SequenceI[] result = importData(resultFile, allOrders);
+        recoverSequences(sequencesHash, result);
+        allResults[job] = result;
+        modelFile.delete();
+        alignmentFile.delete();
+        resultFile.delete();
+      } catch (IOException e)
+      {
+        e.printStackTrace();
+      }
+      job++;
+    }
+
+    String title = "hmmalign to " + hmm.getConsensusSequence().getName();
+    displayResults(allResults, allOrders, msa, title);
+
+    af.setProgressBar("", msgId);
+  }
+
+  /**
+   * Executes the hmmalign command and returns true if successful, false if an
+   * error is detected
+   * 
+   * @param modelFile
+   *          the HMM to align to
+   * @param alignmentFile
+   *          the sequences to align
+   * @param resultFile
+   *          the file to hold the results of alignment
+   * @return
+   * @throws IOException
+   */
+  private boolean runCommand(File modelFile, File alignmentFile,
+          File resultFile) throws IOException
+  {
+    String command = getCommandPath(HMMALIGN);
+    if (command == null)
+    {
+      return false;
+    }
+    List<String> args = new ArrayList<>();
+    args.add(command);
+
+    if (params != null)
+    {
+      for (ArgumentI arg : params)
+      {
+        String name = arg.getName();
+        if (MessageManager.getString("label.trim_termini").equals(name))
+        {
+          args.add(ARG_TRIM);
+        }
+      }
+    }
+    args.add("-o");
+    args.add(resultFile.getAbsolutePath());
+    args.add(modelFile.getAbsolutePath());
+    args.add(alignmentFile.getAbsolutePath());
+    
+    return runCommand(args);
+  }
+
+  /**
+   * Imports the data from the file holding the output of hmmalign
+   * 
+   * @param resultFile
+   * @param allOrders
+   *          a list of alignment orders to add to
+   * 
+   * @return
+   * @throws IOException
+   */
+  private SequenceI[] importData(File resultFile,
+          List<AlignmentOrder> allOrders) throws IOException
+  {
+    StockholmFile file = new StockholmFile(resultFile.getAbsolutePath(),
+            DataSourceType.FILE);
+    SequenceI[] result = file.getSeqsAsArray();
+    AlignmentOrder msaorder = new AlignmentOrder(result);
+    AlignmentSorter.recoverOrder(result);
+    allOrders.add(msaorder);
+
+    return result;
+  }
+
+  /**
+   * Displays the results of all 'jobs' in a new frame
+   * 
+   * @param allResults
+   * 
+   * @param allOrders
+   * @param msa
+   * @param title
+   */
+  private void displayResults(SequenceI[][] allResults,
+          List<AlignmentOrder> allOrders, AlignmentView msa, String title)
+  {
+    AlignmentOrder[] arrOrders = allOrders
+            .toArray(new AlignmentOrder[allOrders.size()]);
+    Object[] newview = msa.getUpdatedView(allResults, arrOrders,
+            alignment.getGapCharacter());
+    SequenceI[] seqs = (SequenceI[]) newview[0];
+    HiddenColumns hidden = (HiddenColumns) newview[1];
+    Alignment al = new Alignment(seqs);
+    al.setProperty("Alignment Program", "hmmalign");
+    if (dataset != null)
+    {
+      al.setDataset(dataset);
+    }
+
+    /*
+     * hack to ensure hmm set on alignment
+     */
+    if (al.getSequenceAt(0).isHMMConsensusSequence())
+    {
+      al.setHmmConsensus(al.getSequenceAt(0));
+    }
+
+    displayInNewFrame(al, allOrders, hidden, title);
+  }
+
+  /**
+   * Displays the results in a new frame
+   * 
+   * @param al
+   *          The alignment containing the results
+   * @param alorders
+   *          The order of the sequences in the alignment on which the jobs were
+   *          run
+   * @param hidden
+   *          Hidden columns in the previous alignment
+   * @param title
+   */
+  private void displayInNewFrame(AlignmentI al,
+          List<AlignmentOrder> alorders, HiddenColumns hidden, String title)
+  {
+    AlignFrame alignFrame = new AlignFrame(al, hidden, AlignFrame.DEFAULT_WIDTH,
+            AlignFrame.DEFAULT_HEIGHT);
+    alignFrame.setTitle(title);
+
+    FeatureRendererSettings featureSettings = af.getFeatureRenderer()
+            .getSettings();
+    // initialise with same renderer settings as in parent alignframe.
+    alignFrame.getFeatureRenderer().transferSettings(featureSettings);
+
+    addSortByMenuItems(alignFrame, alorders);
+
+    // TODO: refactor retrieve and show as new splitFrame as Desktop method
+
+    /*
+     * If alignment was requested from one half of a SplitFrame, show in a
+     * SplitFrame with the other pane similarly aligned.
+     */
+    AlignFrame requestedBy = this.af;
+    if (requestedBy != null && requestedBy.getSplitViewContainer() != null
+            && requestedBy.getSplitViewContainer()
+                    .getComplement(requestedBy) != null)
+    {
+      AlignmentI complement = requestedBy.getSplitViewContainer()
+              .getComplement(requestedBy);
+      String complementTitle = requestedBy.getSplitViewContainer()
+              .getComplementTitle(requestedBy);
+      // becomes null if the alignment window was closed before the alignment
+      // job finished.
+      AlignmentI copyComplement = new Alignment(complement);
+      // todo should this be done by copy constructor?
+      copyComplement.setGapCharacter(complement.getGapCharacter());
+      // share the same dataset (and the mappings it holds)
+      copyComplement.setDataset(complement.getDataset());
+      copyComplement.alignAs(al);
+      if (copyComplement.getHeight() > 0)
+      {
+        alignFrame.setTitle(this.af.getTitle());
+        AlignFrame af2 = new AlignFrame(copyComplement,
+                AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+        af2.setTitle(complementTitle);
+        String linkedTitle = MessageManager
+                .getString("label.linked_view_title");
+        JInternalFrame splitFrame = new SplitFrame(
+                al.isNucleotide() ? alignFrame : af2, al.isNucleotide() ? af2 : alignFrame);
+        Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
+        return;
+      }
+    }
+
+    /*
+     * Not from SplitFrame, or failed to created a complementary alignment
+     */
+    Desktop.addInternalFrame(alignFrame, alignFrame.getTitle(), AlignFrame.DEFAULT_WIDTH,
+            AlignFrame.DEFAULT_HEIGHT);
+  }
+
+  /**
+   * Adds sort order options to the AlignFrame menus
+   * 
+   * @param alignFrame
+   * @param alorders
+   */
+  protected void addSortByMenuItems(AlignFrame alignFrame,
+          List<AlignmentOrder> alorders)
+  {
+    // update orders
+    if (alorders.size() == 1)
+    {
+      alignFrame.addSortByOrderMenuItem("hmmalign" + " Ordering", alorders.get(0));
+    }
+    else
+    {
+      // construct a non-redundant ordering set
+      List<String> names = new ArrayList<>();
+      for (int i = 0, l = alorders.size(); i < l; i++)
+      {
+        String orderName = " Region " + i;
+        int j = i + 1;
+
+        while (j < l)
+        {
+          if (alorders.get(i).equals(alorders.get(j)))
+          {
+            alorders.remove(j);
+            l--;
+            orderName += "," + j;
+          }
+          else
+          {
+            j++;
+          }
+        }
+
+        if (i == 0 && j == 1)
+        {
+          names.add("");
+        }
+        else
+        {
+          names.add(orderName);
+        }
+      }
+      for (int i = 0, l = alorders.size(); i < l; i++)
+      {
+        alignFrame.addSortByOrderMenuItem("hmmalign" + (names.get(i)) + " Ordering",
+                alorders.get(i));
+      }
+    }
+  }
+}
diff --git a/src/jalview/hmmer/HMMBuild.java b/src/jalview/hmmer/HMMBuild.java
new file mode 100644
index 0000000..d95be48
--- /dev/null
+++ b/src/jalview/hmmer/HMMBuild.java
@@ -0,0 +1,362 @@
+package jalview.hmmer;
+
+import jalview.api.AlignViewportI;
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
+import jalview.io.FileParse;
+import jalview.io.HMMFile;
+import jalview.util.MessageManager;
+import jalview.ws.params.ArgumentI;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+
+/**
+ * A class that runs the hmmbuild command as a separate process.
+ * 
+ * @author gmcarstairs
+ *
+ */
+public class HMMBuild extends HmmerCommand
+{
+  static final String ARG_AMINO = "--amino";
+
+  static final String ARG_DNA = "--dna";
+
+  static final String ARG_RNA = "--rna";
+
+  /**
+   * Constructor
+   * 
+   * @param alignFrame
+   * @param args
+   */
+  public HMMBuild(AlignFrame alignFrame, List<ArgumentI> args)
+  {
+    super(alignFrame, args);
+  }
+
+  /**
+   * Builds a HMM from an alignment (and/or groups), then imports and adds it to
+   * the alignment (and/or groups). Call this method directly to execute
+   * synchronously, or via start() in a new Thread for asynchronously.
+   */
+  @Override
+  public void run()
+  {
+    if (params == null || params.isEmpty())
+    {
+      Cache.log.error("No parameters to HMMBuild!|");
+      return;
+    }
+
+    long msgID = System.currentTimeMillis();
+    af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
+            msgID);
+
+    AlignViewportI viewport = af.getViewport();
+    try
+    {
+      /*
+       * run hmmbuild for alignment and/or groups as selected
+       */
+      List<AnnotatedCollectionI> runBuildFor = parseParameters(viewport);
+
+      for (AnnotatedCollectionI grp : runBuildFor)
+      {
+        runHMMBuild(grp);
+      }
+    } finally
+    {
+      af.setProgressBar("", msgID);
+      viewport.alignmentChanged(af.alignPanel);
+      af.buildColourMenu(); // to enable HMMER colour schemes
+    }
+  }
+
+  /**
+   * Scans the parameters to determine whether to run hmmmbuild for the whole
+   * alignment or specified subgroup(s) or both
+   * 
+   * @param viewport
+   * @return
+   */
+  protected List<AnnotatedCollectionI> parseParameters(
+          AlignViewportI viewport)
+  {
+    List<AnnotatedCollectionI> runBuildFor = new ArrayList<>();
+    for (ArgumentI arg : params)
+    {
+      String name = arg.getName();
+      if (MessageManager.getString("label.hmmbuild_for").equals(name))
+      {
+        String value = arg.getValue();
+        if (MessageManager.getString("label.alignment").equals(value))
+        {
+          runBuildFor.add(alignment);
+        }
+        else if (MessageManager.getString("label.groups_and_alignment")
+                .equals(value))
+        {
+          runBuildFor.add(alignment);
+          runBuildFor.addAll(viewport.getAlignment().getGroups());
+        }
+        else if (MessageManager.getString("label.groups").equals(value))
+        {
+          runBuildFor.addAll(viewport.getAlignment().getGroups());
+        }
+        else if (MessageManager.getString("label.selected_group")
+                .equals(value))
+        {
+          runBuildFor.add(viewport.getSelectionGroup());
+        }
+      }
+      else if (MessageManager.getString("label.use_reference")
+              .equals(name))
+      {
+        // todo disable this option if no RF annotation on alignment
+        if (!af.getViewport().hasReferenceAnnotation())
+        {
+          JvOptionPane.showInternalMessageDialog(af, MessageManager
+                  .getString("warn.no_reference_annotation"));
+          // return;
+        }
+      }
+    }
+    return runBuildFor;
+  }
+
+  /**
+   * Runs hmmbuild on the given sequences (alignment or group)
+   * 
+   * @param grp
+   */
+  private void runHMMBuild(AnnotatedCollectionI ac)
+  {
+    File hmmFile = null;
+    File alignmentFile = null;
+    try
+    {
+      hmmFile = createTempFile("hmm", ".hmm");
+      alignmentFile = createTempFile("output", ".sto");
+
+      if (ac instanceof Alignment)
+      {
+        AlignmentI al = (Alignment) ac;
+        // todo pad gaps in an unaligned SequenceGroup as well?
+        if (!al.isAligned())
+        {
+          al.padGaps();
+        }
+      }
+
+      deleteHmmSequences(ac);
+
+      List<SequenceI> copy = new ArrayList<>();
+      if (ac instanceof Alignment)
+      {
+        copy.addAll(ac.getSequences());
+      }
+      else
+      {
+        SequenceI[] sel = ((SequenceGroup) ac)
+                .getSelectionAsNewSequences((AlignmentI) ac.getContext());
+        for (SequenceI seq : sel)
+        {
+          copy.add(seq);
+        }
+      }
+
+      SequenceI[] copyArray = copy.toArray(new SequenceI[copy.size()]);
+      Hashtable sequencesHash = stashSequences(copyArray);
+
+      exportStockholm(copyArray, alignmentFile, ac);
+
+      recoverSequences(sequencesHash, copy.toArray(new SequenceI[] {}));
+
+      boolean ran = runCommand(alignmentFile, hmmFile, ac);
+      if (!ran)
+      {
+        return;
+      }
+      importData(hmmFile, ac);
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+    } finally
+    {
+      if (hmmFile != null)
+      {
+        hmmFile.delete();
+      }
+      if (alignmentFile != null)
+      {
+        alignmentFile.delete();
+      }
+    }
+  }
+
+  /**
+   * A helper method that deletes any HMM consensus sequence from the given
+   * collection, and from the parent alignment if <code>ac</code> is a subgroup
+   * 
+   * @param ac
+   */
+  void deleteHmmSequences(AnnotatedCollectionI ac)
+  {
+    SequenceI hmmSeq = ac.getHmmConsensus();
+    if (hmmSeq != null)
+    {
+      if (ac instanceof SequenceGroup)
+      {
+        ((SequenceGroup) ac).deleteSequence(hmmSeq, false);
+        AnnotatedCollectionI context = ac.getContext();
+        if (context != null && context instanceof AlignmentI)
+        {
+          ((AlignmentI) context).deleteSequence(hmmSeq);
+        }
+      }
+      else
+      {
+        ((AlignmentI) ac).deleteSequence(hmmSeq);
+      }
+    }
+  }
+
+  /**
+   * Constructs and executes the hmmbuild command as a separate process
+   * 
+   * @param sequencesFile
+   *          the alignment from which the HMM is built
+   * @param hmmFile
+   *          the output file to which the HMM is written
+   * @param group
+   *          alignment or group for which the hmm is generated
+   * 
+   * @return
+   * @throws IOException
+   */
+  private boolean runCommand(File sequencesFile, File hmmFile,
+          AnnotatedCollectionI group) throws IOException
+  {
+    String cmd = getCommandPath(HMMBUILD);
+    if (cmd == null)
+    {
+      return false; // executable not found
+    }
+    List<String> args = new ArrayList<>();
+    args.add(cmd);
+
+    /*
+     * HMM name (will be given to consensus sequence) is
+     * - as specified by an input parameter if set
+     * - else group name with _HMM appended (if for a group)
+     * - else align frame title with _HMM appended (if title is not too long)
+     * - else "Alignment_HMM" 
+     */
+    String name = "";
+
+    if (params != null)
+    {
+      for (ArgumentI arg : params)
+      {
+        String argName = arg.getName();
+        switch (argName)
+        {
+        case "HMM Name":
+          name = arg.getValue().trim();
+          break;
+        case "Use Reference Annotation":
+          args.add("--hand");
+          break;
+        }
+      }
+    }
+
+    if (group instanceof SequenceGroup)
+    {
+      name = ((SequenceGroup) group).getName() + "_HMM";
+    }
+
+    if ("".equals(name))
+    {
+      if (af != null && af.getTitle().length() < 15)
+      {
+        name = af.getTitle();
+      }
+      else
+      {
+        name = "Alignment_HMM";
+      }
+    }
+
+    args.add("-n");
+    args.add(name.replace(' ', '_'));
+    if (!alignment.isNucleotide())
+    {
+      args.add(ARG_AMINO); // TODO check for rna
+    }
+    else
+    {
+      args.add(ARG_DNA);
+    }
+
+    args.add(hmmFile.getAbsolutePath());
+    args.add(sequencesFile.getAbsolutePath());
+
+    return runCommand(args);
+  }
+
+  /**
+   * Imports the .hmm file produced by hmmbuild, and inserts the HMM consensus
+   * sequence (with attached HMM profile) as the first sequence in the alignment
+   * or group for which it was generated
+   * 
+   * @param hmmFile
+   * @param ac
+   *          (optional) the group for which the hmm was generated
+   * @throws IOException
+   */
+  private void importData(File hmmFile, AnnotatedCollectionI ac)
+          throws IOException
+  {
+    HMMFile file = new HMMFile(
+            new FileParse(hmmFile.getAbsolutePath(), DataSourceType.FILE));
+    SequenceI hmmSeq = file.getHMM().getConsensusSequence();
+
+    if (ac instanceof SequenceGroup)
+    {
+      SequenceGroup grp = (SequenceGroup) ac;
+      char gapChar = alignment.getGapCharacter();
+      hmmSeq.insertCharAt(0, ac.getStartRes(), gapChar);
+      hmmSeq.insertCharAt(ac.getEndRes() + 1,
+              alignment.getWidth() - ac.getEndRes() - 1, gapChar);
+      SequenceI topSeq = grp.getSequencesInOrder(alignment)[0];
+      int topIndex = alignment.findIndex(topSeq);
+      alignment.insertSequenceAt(topIndex, hmmSeq);
+      ac.setSeqrep(hmmSeq);
+      grp.addSequence(hmmSeq, false);
+      grp.setHmmConsensus(hmmSeq);
+    }
+    else
+    {
+      alignment.insertSequenceAt(0, hmmSeq);
+      alignment.setHmmConsensus(hmmSeq);
+    }
+
+    if (af.getSelectedHMM() == null)
+    {
+      af.setSelectedHMMSequence(hmmSeq);
+    }
+  }
+}
diff --git a/src/jalview/hmmer/HMMERParamStore.java b/src/jalview/hmmer/HMMERParamStore.java
new file mode 100644
index 0000000..c668481
--- /dev/null
+++ b/src/jalview/hmmer/HMMERParamStore.java
@@ -0,0 +1,225 @@
+package jalview.hmmer;
+
+import jalview.bin.Cache;
+import jalview.gui.Preferences;
+import jalview.util.MessageManager;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.ParamDatastoreI;
+import jalview.ws.params.WsParamSetI;
+import jalview.ws.params.simple.BooleanOption;
+import jalview.ws.params.simple.IntegerParameter;
+import jalview.ws.params.simple.LogarithmicParameter;
+import jalview.ws.params.simple.Option;
+import jalview.ws.params.simple.StringParameter;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.Scanner;
+
+public final class HMMERParamStore implements ParamDatastoreI
+{
+  private static final String HMMBUILD = "hmmbuild";
+
+  private static final String HMMALIGN = "hmmalign";
+
+  private static final String HMMSEARCH = "hmmsearch";
+
+  String name;
+
+  List<WsParamSetI> presets = new ArrayList<>();
+
+  private HMMERParamStore(String nam)
+  {
+    this.name = nam;
+  }
+
+  public static HMMERParamStore forBuild()
+  {
+    return new HMMERParamStore(HMMBUILD);
+  }
+
+  public static HMMERParamStore forAlign()
+  {
+    return new HMMERParamStore(HMMALIGN);
+  }
+
+  public static HMMERParamStore forSearch()
+  {
+    return new HMMERParamStore(HMMSEARCH);
+  }
+
+  @Override
+  public List<WsParamSetI> getPresets()
+  {
+    return presets;
+  }
+
+  @Override
+  public WsParamSetI getPreset(String nam)
+  {
+    return null;
+  }
+
+  @Override
+  public List<ArgumentI> getServiceParameters()
+  {
+    List<ArgumentI> args = new ArrayList<>();
+    switch (name)
+    {
+    case HMMSEARCH:
+      getHMMSearchParams(args);
+      break;
+    case HMMALIGN:
+      getHMMAlignParams(args);
+      break;
+    case HMMBUILD:
+      getHMMBuildParams(args);
+      break;
+    default:
+    }
+
+    return args;
+  }
+
+  private void getHMMSearchParams(List<ArgumentI> args)
+  {
+    args.add(new IntegerParameter(
+            MessageManager.getString("label.number_of_results"),
+            MessageManager.getString("label.number_of_results_desc"), true,
+            100, 0, 100000));
+    String names = Cache.getProperty(Preferences.HMMSEARCH_DBS);
+    if (names != null && !names.isEmpty())
+    {
+      Collection<String> databases = new ArrayList<>();
+      databases.add(MessageManager.getString("label.this_alignment"));
+      Scanner nameScanner = new Scanner(names);
+
+      if (nameScanner.hasNext())
+      {
+        while (nameScanner.hasNext())
+        {
+          String next = nameScanner.next();
+          if ("null".equals(next))
+          {
+            Cache.setProperty(Preferences.HMMSEARCH_DBS, "");
+            Cache.setProperty(Preferences.HMMSEARCH_DB_PATHS, "");
+          }
+          else
+          {
+            databases.add(next);
+          }
+        }
+      }
+      nameScanner.close();
+      args.add(new Option(MessageManager.getString("label.database"),
+              MessageManager.getString("label.database_for_hmmsearch"),
+              true, MessageManager.getString("label.this_alignment"),
+              MessageManager.getString("label.this_alignment"), databases,
+              null));
+    }
+    args.add(new BooleanOption(
+            MessageManager.getString("label.auto_align_seqs"),
+            MessageManager.getString("label.auto_align_seqs_desc"), false,
+            false, true, null));
+    args.add(new BooleanOption(
+            MessageManager.getString("label.use_accessions"),
+            MessageManager.getString("label.use_accessions_desc"), false,
+            false, true, null));
+    args.add(new BooleanOption(
+            MessageManager.getString("label.trim_termini"),
+            MessageManager.getString("label.trim_termini_desc"), false,
+            false, true, null));
+    args.add(new LogarithmicParameter(
+            MessageManager.getString("label.seq_e_value"),
+            MessageManager.getString("label.seq_e_value_desc"), false, -3d,
+            -37.92977945, 1d, 10d));
+    /*
+    args.add(new DoubleParameter(
+            MessageManager.getString("label.seq_score"),
+            MessageManager.getString("label.seq_score_desc"), false,
+            0d, 0d, 10000d));
+       */
+    args.add(new LogarithmicParameter(
+            MessageManager.getString("label.dom_e_value_desc"),
+            MessageManager.getString("label.dom_e_value_desc"), false, -3d,
+            -37.92977945, 1d, 10d));
+    /*
+    args.add(new DoubleParameter(
+            MessageManager.getString("label.dom_score"),
+            MessageManager.getString("label.dom_score_desc"), false, 0d,
+            0d,
+            10000d));
+            */
+  }
+
+  private void getHMMAlignParams(List<ArgumentI> args)
+  {
+    args.add(new BooleanOption(
+            MessageManager.getString("label.trim_termini"),
+            MessageManager.getString("label.trim_termini_desc"),
+            false, false, true, null));
+  }
+
+  private void getHMMBuildParams(List<ArgumentI> args)
+  {
+    args.add(new StringParameter(MessageManager.getString("label.hmm_name"),
+            MessageManager.getString("label.hmm_name_desc"), true, ""));
+    // todo only enable Use Reference Annotation if RF is present
+    args.add(new BooleanOption(
+            MessageManager.getString("label.use_reference"),
+            MessageManager.getString("label.use_reference_desc"), true,
+            true, true, null));
+
+    Collection<String> options = new ArrayList<>();
+    options.add(MessageManager.getString("label.alignment"));
+    options.add(MessageManager.getString("label.groups_and_alignment"));
+    options.add(MessageManager.getString("label.groups"));
+    options.add(MessageManager.getString("label.selected_group"));
+
+    args.add(new Option(MessageManager.getString("label.hmmbuild_for"),
+            MessageManager.getString("label.hmmbuild_for_desc"), true,
+            MessageManager.getString("label.alignment"),
+            MessageManager.getString("label.alignment"), options, null));
+  }
+
+  @Override
+  public boolean presetExists(String forName)
+  {
+    return false;
+  }
+
+  @Override
+  public void deletePreset(String forName)
+  {
+  }
+
+  @Override
+  public void storePreset(String presetName, String text,
+          List<ArgumentI> jobParams)
+  {
+  }
+
+  @Override
+  public void updatePreset(String oldName, String presetName, String text,
+          List<ArgumentI> jobParams)
+  {
+  }
+
+  @Override
+  public WsParamSetI parseServiceParameterFile(String forName,
+          String description, String[] serviceURL, String parameters)
+          throws IOException
+  {
+    return null;
+  }
+
+  @Override
+  public String generateServiceParameterFile(WsParamSetI pset)
+          throws IOException
+  {
+    return null;
+  }
+
+}
diff --git a/src/jalview/hmmer/HMMERPreset.java b/src/jalview/hmmer/HMMERPreset.java
new file mode 100644
index 0000000..2712259
--- /dev/null
+++ b/src/jalview/hmmer/HMMERPreset.java
@@ -0,0 +1,57 @@
+package jalview.hmmer;
+
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.WsParamSetI;
+
+import java.util.List;
+
+public class HMMERPreset implements WsParamSetI
+{
+
+  @Override
+  public String getName()
+  {
+    return null;
+  }
+
+  @Override
+  public String getDescription()
+  {
+    return null;
+  }
+
+  @Override
+  public String[] getApplicableUrls()
+  {
+    return null;
+  }
+
+  @Override
+  public String getSourceFile()
+  {
+    return null;
+  }
+
+  @Override
+  public void setSourceFile(String newfile)
+  {
+  }
+
+  @Override
+  public boolean isModifiable()
+  {
+    return false;
+  }
+
+  @Override
+  public List<ArgumentI> getArguments()
+  {
+    return null;
+  }
+
+  @Override
+  public void setArguments(List<ArgumentI> args)
+  {
+  }
+
+}
diff --git a/src/jalview/hmmer/HMMSearch.java b/src/jalview/hmmer/HMMSearch.java
new file mode 100644
index 0000000..30299e9
--- /dev/null
+++ b/src/jalview/hmmer/HMMSearch.java
@@ -0,0 +1,320 @@
+package jalview.hmmer;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenMarkovModel;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
+import jalview.io.FileParse;
+import jalview.io.StockholmFile;
+import jalview.util.MessageManager;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.simple.BooleanOption;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Scanner;
+
+import javax.swing.JOptionPane;
+
+public class HMMSearch extends HmmerCommand
+{
+  static final String HMMSEARCH = "hmmsearch";
+
+  boolean realign = false;
+
+  boolean trim = false;
+
+  int seqsToReturn = Integer.MAX_VALUE;
+
+  SequenceI[] seqs;
+
+  /**
+   * Constructor for the HMMSearchThread
+   * 
+   * @param af
+   */
+  public HMMSearch(AlignFrame af, List<ArgumentI> args)
+  {
+    super(af, args);
+  }
+
+  /**
+   * Runs the HMMSearchThread: the data on the alignment or group is exported,
+   * then the command is executed in the command line and then the data is
+   * imported and displayed in a new frame. Call this method directly to execute
+   * synchronously, or via start() in a new Thread for asynchronously.
+   */
+  @Override
+  public void run()
+  {
+    HiddenMarkovModel hmm = af.getSelectedHMM();
+    if (hmm == null)
+    {
+      JOptionPane.showMessageDialog(af,
+              MessageManager.getString("warn.no_selected_hmm"));
+      return;
+    }
+
+    SequenceI hmmSeq = af.getSelectedHMMSequence();
+    long msgId = System.currentTimeMillis();
+    af.setProgressBar(MessageManager.getString("status.running_hmmsearch"),
+            msgId);
+
+    try
+    {
+      File hmmFile = createTempFile("hmm", ".hmm");
+      File hitsAlignmentFile = createTempFile("hitAlignment", ".sto");
+      File searchOutputFile = createTempFile("searchOutput", ".sto");
+
+      exportHmm(hmm, hmmFile.getAbsoluteFile());
+
+      boolean ran = runCommand(searchOutputFile, hitsAlignmentFile, hmmFile);
+      if (!ran)
+      {
+        JvOptionPane.showInternalMessageDialog(af,
+                MessageManager.getString("warn.hmmsearch_failed"));
+        return;
+      }
+
+      importData(hmmSeq, hitsAlignmentFile, hmmFile, searchOutputFile);
+      // TODO make realignment of search results a step at this level
+      // and make it conditional on this.realign
+    } catch (IOException | InterruptedException e)
+    {
+      e.printStackTrace();
+    }
+    finally
+    {
+      af.setProgressBar("", msgId);
+    }
+  }
+
+  /**
+   * Executes an hmmsearch with the given hmm as input. The database to be
+   * searched is a local file as specified by the 'Database' parameter, or the
+   * current alignment (written to file) if none is specified.
+   * 
+   * @param searchOutputFile
+   * @param hitsAlignmentFile
+   * @param hmmFile
+   * 
+   * @return
+   * @throws IOException
+   */
+  private boolean runCommand(File searchOutputFile, File hitsAlignmentFile,
+          File hmmFile) throws IOException
+  {
+    String command = getCommandPath(HMMSEARCH);
+    if (command == null)
+    {
+      return false;
+    }
+
+    List<String> args = new ArrayList<>();
+    args.add(command);
+    args.add("-o");
+    args.add(searchOutputFile.getAbsolutePath());
+    args.add("-A");
+    args.add(hitsAlignmentFile.getAbsolutePath());
+
+    boolean dbFound = false;
+    String dbPath = "";
+    File databaseFile = null;
+
+    if (params != null)
+    {
+      for (ArgumentI arg : params)
+      {
+        String name = arg.getName();
+        if (MessageManager.getString("label.number_of_results")
+                .equals(name))
+        {
+          seqsToReturn = Integer.parseInt(arg.getValue());
+        }
+        else if (MessageManager.getString("label.auto_align_seqs")
+                .equals(name))
+        {
+          realign = true; // TODO: not used
+        }
+        else if (MessageManager.getString("label.use_accessions")
+                .equals(name))
+        {
+          args.add("--acc");
+        }
+        else if (MessageManager.getString("label.seq_e_value").equals(name))
+        {
+          args.add("--incE");
+          args.add(arg.getValue());
+        }
+        else if (MessageManager.getString("label.seq_score").equals(name))
+        {
+          args.add("-incT");
+          args.add(arg.getValue());
+        }
+        else if (MessageManager.getString("label.dom_e_value_desc")
+                .equals(name))
+        {
+          args.add("--incdomE");
+          args.add(arg.getValue());
+        }
+        else if (MessageManager.getString("label.dom_score").equals(name))
+        {
+          args.add("--incdomT");
+          args.add(arg.getValue());
+        }
+        else if (MessageManager.getString("label.trim_termini")
+                .equals(name))
+        {
+          trim = true;
+        }
+        else if (MessageManager.getString("label.database").equals(name))
+        {
+          dbFound = true;
+          dbPath = arg.getValue();
+          if (!MessageManager.getString("label.this_alignment")
+                  .equals(dbPath))
+          {
+            databaseFile = new File(dbPath);
+          }
+        }
+      }
+    }
+
+    if (!dbFound || MessageManager.getString("label.this_alignment")
+            .equals(dbPath))
+    {
+      /*
+       * no external database specified for search, so
+       * export current alignment as 'database' to search
+       */
+      databaseFile = createTempFile("database", ".sto");
+      AlignmentI al = af.getViewport().getAlignment();
+      AlignmentI copy = new Alignment(al);
+      SequenceI hmms = copy.getHmmConsensus();
+      if (hmms != null)
+      {
+        copy.deleteSequence(hmms);
+      }
+      exportStockholm(copy.getSequencesArray(), databaseFile, null);
+      // StockholmFile stoFile = new StockholmFile(copy);
+      // stoFile.setSeqs(copy.getSequencesArray());
+      // String alignmentString = stoFile.print();
+      // PrintWriter writer = new PrintWriter(databaseFile);
+      // writer.print(alignmentString);
+      // writer.close();
+    }
+
+    args.add(hmmFile.getAbsolutePath());
+    args.add(databaseFile.getAbsolutePath());
+
+    return runCommand(args);
+  }
+
+  /**
+   * Imports the data from the temporary file to which the output of hmmsearch
+   * is directed.
+   * 
+   * @param hmmSeq
+   */
+  private void importData(SequenceI hmmSeq, File inputAlignmentTemp,
+          File hmmTemp, File searchOutputFile)
+          throws IOException, InterruptedException
+  {
+    BufferedReader br = new BufferedReader(
+            new FileReader(inputAlignmentTemp));
+    try
+    {
+      if (br.readLine() == null)
+      {
+        JOptionPane.showMessageDialog(af,
+                MessageManager.getString("label.no_sequences_found"));
+        return;
+      }
+      StockholmFile file = new StockholmFile(new FileParse(
+              inputAlignmentTemp.getAbsolutePath(), DataSourceType.FILE));
+      seqs = file.getSeqsAsArray();
+
+      readTable(searchOutputFile);
+
+      int seqCount = Math.min(seqs.length, seqsToReturn);
+      SequenceI[] hmmAndSeqs = new SequenceI[seqCount + 1];
+      hmmAndSeqs[0] = hmmSeq;
+      System.arraycopy(seqs, 0, hmmAndSeqs, 1, seqCount);
+
+      AlignmentI alignment = new Alignment(hmmAndSeqs);
+      AlignFrame frame = new AlignFrame(alignment, 1, 1);
+      frame.setSelectedHMMSequence(hmmSeq);
+      List<ArgumentI> alignArgs = new ArrayList<>();
+      if (trim)
+      {
+        alignArgs.add(new BooleanOption(
+                MessageManager.getString("label.trim_termini"),
+                MessageManager.getString("label.trim_termini_desc"), true,
+                true, true, null));
+      }
+      HMMAlign hmmalign = new HMMAlign(frame, alignArgs);
+      hmmalign.run();
+      frame = null;
+      hmmTemp.delete();
+      inputAlignmentTemp.delete();
+      searchOutputFile.delete();
+    } finally
+    {
+      if (br != null)
+      {
+        br.close();
+      }
+    }
+  }
+
+  void readTable(File inputTableTemp) throws IOException
+  {
+    BufferedReader br = new BufferedReader(new FileReader(inputTableTemp));
+    String line = "";
+    while (!line.startsWith("Query:"))
+    {
+      line = br.readLine();
+    }
+    for (int i = 0; i < 5; i++)
+    {
+      line = br.readLine();
+    }
+
+    int index = 0;
+    while (!"  ------ inclusion threshold ------".equals(line)
+            && !"".equals(line))
+    {
+      Scanner scanner = new Scanner(line);
+
+      String str = scanner.next(); // full sequence eValue score
+      float eValue = Float.parseFloat(str);
+      int seqLength = seqs[index].getLength();
+      Annotation[] annots = new Annotation[seqLength];
+      for (int j = 0; j < seqLength; j++)
+      {
+        annots[j] = new Annotation(eValue);
+      }
+      AlignmentAnnotation annot = new AlignmentAnnotation("E-value",
+              "Score", annots);
+      annot.setScore(Double.parseDouble(str));
+      annot.setSequenceRef(seqs[index]);
+      seqs[index].addAlignmentAnnotation(annot);
+
+      scanner.close();
+      line = br.readLine();
+      index++;
+    }
+
+    br.close();
+  }
+
+}
diff --git a/src/jalview/hmmer/HmmerCommand.java b/src/jalview/hmmer/HmmerCommand.java
new file mode 100644
index 0000000..fe6c0f9
--- /dev/null
+++ b/src/jalview/hmmer/HmmerCommand.java
@@ -0,0 +1,280 @@
+package jalview.hmmer;
+
+import jalview.analysis.SeqsetUtils;
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenMarkovModel;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
+import jalview.gui.Preferences;
+import jalview.io.HMMFile;
+import jalview.io.StockholmFile;
+import jalview.util.MessageManager;
+import jalview.ws.params.ArgumentI;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.PrintWriter;
+import java.util.Hashtable;
+import java.util.List;
+
+/**
+ * Base class for hmmbuild, hmmalign and hmmsearch
+ * 
+ * @author TZVanaalten
+ *
+ */
+public abstract class HmmerCommand implements Runnable
+{
+  public static final String HMMBUILD = "hmmbuild";
+
+  protected final AlignFrame af;
+
+  protected final AlignmentI alignment;
+
+  protected final List<ArgumentI> params;
+
+  /**
+   * Constructor
+   * 
+   * @param alignFrame
+   * @param args
+   */
+  public HmmerCommand(AlignFrame alignFrame, List<ArgumentI> args)
+  {
+    af = alignFrame;
+    alignment = af.getViewport().getAlignment();
+    params = args;
+  }
+
+  /**
+   * Answers true if preference HMMER_PATH is set, and its value is the path to
+   * a directory that contains an executable <code>hmmbuild</code> or
+   * <code>hmmbuild.exe</code>, else false
+   * 
+   * @return
+   */
+  public static boolean isHmmerAvailable()
+  {
+    File exec = getExecutable(HMMBUILD, Cache.getProperty(Preferences.HMMER_PATH));
+    return exec != null;
+  }
+
+  /**
+   * Uniquifies the sequences when exporting and stores their details in a
+   * hashtable
+   * 
+   * @param seqs
+   */
+  protected Hashtable stashSequences(SequenceI[] seqs)
+  {
+    return SeqsetUtils.uniquify(seqs, true);
+  }
+
+  /**
+   * Restores the sequence data lost by uniquifying
+   * 
+   * @param hashtable
+   * @param seqs
+   */
+  protected void recoverSequences(Hashtable hashtable, SequenceI[] seqs)
+  {
+    SeqsetUtils.deuniquify(hashtable, seqs);
+  }
+
+  /**
+   * Runs a command as a separate process and waits for it to complete. Answers
+   * true if the process return status is zero, else false.
+   * 
+   * @param command
+   *          the executable command and any arguments to it
+   * @throws IOException
+   */
+  public boolean runCommand(List<String> command)
+          throws IOException
+  {
+    try
+    {
+      ProcessBuilder pb = new ProcessBuilder(command);
+      pb.redirectErrorStream(true); // merge syserr to sysout
+      final Process p = pb.start();
+      new Thread(new Runnable()
+      {
+        @Override
+        public void run()
+        {
+          BufferedReader input = new BufferedReader(
+                  new InputStreamReader(p.getInputStream()));
+          try
+          {
+            String line = input.readLine();
+            while (line != null)
+            {
+              System.out.println(line);
+              line = input.readLine();
+            }
+          } catch (IOException e)
+          {
+            e.printStackTrace();
+          }
+        }
+      }).start();
+
+      p.waitFor();
+      return p.exitValue() == 0; // 0 is success, by convention
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+      return false;
+    }
+  }
+
+  /**
+   * Exports an alignment, and reference (RF) annotation if present, to the
+   * specified file, in Stockholm format
+   * 
+   * @param seqs
+   * @param toFile
+   * @param annotated
+   * @throws IOException
+   */
+  public void exportStockholm(SequenceI[] seqs, File toFile,
+          AnnotatedCollectionI annotated) throws IOException
+  {
+    if (seqs == null)
+    {
+      return;
+    }
+    AlignmentI newAl = new Alignment(seqs);
+    if (!newAl.isAligned())
+    {
+      newAl.padGaps();
+    }
+
+    if (toFile != null && annotated != null)
+    {
+      AlignmentAnnotation[] annots = annotated.getAlignmentAnnotation();
+      if (annots != null)
+      {
+        for (AlignmentAnnotation annot : annots)
+        {
+          if (annot.label.contains("Reference") || "RF".equals(annot.label))
+          {
+            AlignmentAnnotation newRF;
+            if (annot.annotations.length > newAl.getWidth())
+            {
+              Annotation[] rfAnnots = new Annotation[newAl.getWidth()];
+              System.arraycopy(annot.annotations, 0, rfAnnots, 0,
+                      rfAnnots.length);
+              newRF = new AlignmentAnnotation("RF", "Reference Positions",
+                      rfAnnots);
+            }
+            else
+            {
+              newRF = new AlignmentAnnotation(annot);
+            }
+            newAl.addAnnotation(newRF);
+          }
+        }
+      }
+    }
+
+    StockholmFile file = new StockholmFile(newAl);
+    String output = file.print(seqs, false);
+    PrintWriter writer = new PrintWriter(toFile);
+    writer.println(output);
+    writer.close();
+  }
+
+  /**
+   * Answers the full path to the given hmmer executable, or null if file cannot
+   * be found or is not executable
+   * 
+   * @param cmd
+   *          command short name e.g. hmmalign
+   * @return
+   */
+  protected String getCommandPath(String cmd)
+  {
+    String binariesFolder = Cache.getProperty(Preferences.HMMER_PATH);
+    File file = getExecutable(cmd, binariesFolder);
+    if (file == null && af != null)
+    {
+        JvOptionPane.showInternalMessageDialog(af,
+                MessageManager.getString("warn.hmm_command_failed"));
+    }
+
+    return file == null ? null : file.getAbsolutePath();
+  }
+
+  /**
+   * Answers the executable file for the given hmmer command, or null if not
+   * found or not executable. The path to the executable is the command name
+   * prefixed by the hmmer binaries folder path, optionally with .exe appended.
+   * 
+   * @param cmd
+   *          hmmer command short name, for example hmmbuild
+   * @param binaryPath
+   *          parent folder containing hmmer executables
+   * @return
+   */
+  public static File getExecutable(String cmd, String binaryPath)
+  {
+    File file = new File(binaryPath, cmd);
+    if (!file.canExecute())
+    {
+      file = new File(binaryPath, cmd + ".exe");
+      {
+        if (!file.canExecute())
+        {
+          file = null;
+        }
+      }
+    }
+    return file;
+  }
+
+  /**
+   * A convenience method to create a temporary file that is deleted on exit of
+   * the JVM
+   * 
+   * @param prefix
+   * @param suffix
+   * @return
+   * @throws IOException
+   */
+  protected File createTempFile(String prefix, String suffix)
+          throws IOException
+  {
+    File f = File.createTempFile(prefix, suffix);
+    f.deleteOnExit();
+    return f;
+
+  }
+
+  /**
+   * Exports an HMM to the specified file
+   * 
+   * @param hmm
+   * @param hmmFile
+   * @throws IOException
+   */
+  public void exportHmm(HiddenMarkovModel hmm, File hmmFile)
+          throws IOException
+  {
+    if (hmm != null)
+    {
+      HMMFile file = new HMMFile(hmm);
+      PrintWriter writer = new PrintWriter(hmmFile);
+      writer.print(file.print());
+      writer.close();
+    }
+  }
+}
diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 2340283..dcdf98e 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -304,9 +304,9 @@ public abstract class AlignFile extends FileParse
    */
   protected void initData()
   {
-    seqs = new Vector<SequenceI>();
-    annotations = new Vector<AlignmentAnnotation>();
-    seqGroups = new ArrayList<SequenceGroup>();
+    seqs = new Vector<>();
+    annotations = new Vector<>();
+    seqGroups = new ArrayList<>();
     parseCalled = false;
   }
 
@@ -319,7 +319,7 @@ public abstract class AlignFile extends FileParse
   @Override
   public void setSeqs(SequenceI[] s)
   {
-    seqs = new Vector<SequenceI>();
+    seqs = new Vector<>();
 
     for (int i = 0; i < s.length; i++)
     {
@@ -390,7 +390,7 @@ public abstract class AlignFile extends FileParse
   {
     if (newickStrings == null)
     {
-      newickStrings = new Vector<String[]>();
+      newickStrings = new Vector<>();
     }
     newickStrings.addElement(new String[] { treeName, newickString });
   }
@@ -414,4 +414,16 @@ public abstract class AlignFile extends FileParse
   {
     seqs.add(seq);
   }
+
+  /**
+   * Used only for hmmer statistics, so should probably be removed at some
+   * point. TODO remove this
+   * 
+   * @return
+   */
+  public Vector<AlignmentAnnotation> getAnnotations()
+  {
+    return annotations;
+  }
+
 }
diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 00476d6..e578a45 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -968,7 +968,7 @@ public class AnnotationFile
             else
             {
               // consider deferring this till after the file has been parsed ?
-              hidden.hideInsertionsFor(sr);
+              hidden.hideList(sr.getInsertions());
             }
           }
           modified = true;
diff --git a/src/jalview/io/FileFormat.java b/src/jalview/io/FileFormat.java
index 4b33dbf..6ff5461 100644
--- a/src/jalview/io/FileFormat.java
+++ b/src/jalview/io/FileFormat.java
@@ -373,8 +373,24 @@ public enum FileFormat implements FileFormatI
     {
       return false;
     }
+  },
+  HMMER3("HMMER3", "hmm", true, true)
+  {
+    @Override
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
+    {
+      return new HMMFile(source);
+    }
+
+    @Override
+    public AlignmentFileWriterI getWriter(AlignmentI al)
+    {
+      return new HMMFile();
+    }
   };
 
+
   private boolean writable;
 
   private boolean readable;
diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index f26d6da..2d753c1 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -199,6 +199,32 @@ public class FileLoader implements Runnable
     return alignFrame;
   }
 
+  public void LoadFileOntoAlignmentWaitTillLoaded(AlignViewport viewport,
+          String file, DataSourceType sourceType, FileFormatI format)
+  {
+    this.viewport = viewport;
+    this.file = file;
+    this.protocol = sourceType;
+    this.format = format;
+    _LoadAlignmentFileWaitTillLoaded();
+  }
+
+  protected void _LoadAlignmentFileWaitTillLoaded()
+  {
+    Thread loader = new Thread(this);
+    loader.start();
+
+    while (loader.isAlive())
+    {
+      try
+      {
+        Thread.sleep(500);
+      } catch (Exception ex)
+      {
+      }
+    }
+  }
+
   public void updateRecentlyOpened()
   {
     Vector recent = new Vector();
@@ -394,6 +420,23 @@ public class FileLoader implements Runnable
             }
             // append to existing alignment
             viewport.addAlignment(al, title);
+            if (source instanceof HMMFile)
+            {
+              AlignmentI alignment = viewport.getAlignment();
+              SequenceI seq = alignment
+                      .getSequenceAt(alignment.getAbsoluteHeight() - 1);
+              if (seq.isHMMConsensusSequence())
+              {
+                /* 
+                 * fudge: move HMM consensus sequence from last to first
+                 */
+                alignment.deleteSequence(alignment.getAbsoluteHeight() - 1);
+                alignment.insertSequenceAt(0, seq);
+                alignment.setHmmConsensus(seq);
+              }
+              viewport.getAlignPanel().adjustAnnotationHeight();
+              viewport.updateSequenceIdColours();
+            }
           }
           else
           {
diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 7647a16..6d3c18a 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -212,12 +212,12 @@ public class FormatAdapter extends AppletFormatAdapter
           AlignmentAnnotation na = new AlignmentAnnotation(ala[i]);
           if (selgp != null)
           {
-            hidden.makeVisibleAnnotation(selgp.getStartRes(),
-                    selgp.getEndRes(), na);
+            na.makeVisibleAnnotation(selgp.getStartRes(), selgp.getEndRes(),
+                    hidden);
           }
           else
           {
-            hidden.makeVisibleAnnotation(na);
+            na.makeVisibleAnnotation(hidden);
           }
           alv.addAnnotation(na);
         }
diff --git a/src/jalview/io/HMMFile.java b/src/jalview/io/HMMFile.java
new file mode 100644
index 0000000..2a17915
--- /dev/null
+++ b/src/jalview/io/HMMFile.java
@@ -0,0 +1,717 @@
+package jalview.io;
+
+import jalview.api.AlignExportSettingI;
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.HMMNode;
+import jalview.datamodel.HiddenMarkovModel;
+import jalview.datamodel.SequenceI;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Scanner;
+
+
+/**
+ * Adds capability to read in and write out HMMER3 files. .
+ * 
+ * 
+ * @author TZVanaalten
+ *
+ */
+public class HMMFile extends AlignFile
+        implements AlignmentFileReaderI, AlignmentFileWriterI
+{
+  private static final String TERMINATOR = "//";
+
+  /*
+   * keys to data in HMM file, used to store as properties of the HiddenMarkovModel
+   */
+  public static final String HMM = "HMM";
+
+  public static final String NAME = "NAME";
+
+  public static final String ACCESSION_NUMBER = "ACC";
+
+  public static final String DESCRIPTION = "DESC";
+
+  public static final String LENGTH = "LENG";
+
+  public static final String MAX_LENGTH = "MAXL";
+
+  public static final String ALPHABET = "ALPH";
+
+  public static final String DATE = "DATE";
+
+  public static final String COMMAND_LOG = "COM";
+
+  public static final String NUMBER_OF_SEQUENCES = "NSEQ";
+
+  public static final String EFF_NUMBER_OF_SEQUENCES = "EFFN";
+
+  public static final String CHECK_SUM = "CKSUM";
+
+  public static final String STATISTICS = "STATS";
+
+  public static final String COMPO = "COMPO";
+
+  public static final String GATHERING_THRESHOLD = "GA";
+
+  public static final String TRUSTED_CUTOFF = "TC";
+
+  public static final String NOISE_CUTOFF = "NC";
+
+  public static final String VITERBI = "VITERBI";
+
+  public static final String MSV = "MSV";
+
+  public static final String FORWARD = "FORWARD";
+
+  public static final String MAP = "MAP";
+
+  public static final String REFERENCE_ANNOTATION = "RF";
+
+  public static final String CONSENSUS_RESIDUE = "CONS";
+
+  public static final String CONSENSUS_STRUCTURE = "CS";
+
+  public static final String MASKED_VALUE = "MM";
+
+  private static final String ALPH_AMINO = "amino";
+
+  private static final String ALPH_DNA = "DNA";
+
+  private static final String ALPH_RNA = "RNA";
+
+  private static final String ALPHABET_AMINO = "ACDEFGHIKLMNPQRSTVWY";
+
+  private static final String ALPHABET_DNA = "ACGT";
+
+  private static final String ALPHABET_RNA = "ACGU";
+
+  private static final int NUMBER_OF_TRANSITIONS = 7;
+
+  private static final String SPACE = " ";
+
+  /*
+   * optional guide line added to an output HMMER file, purely for readability
+   */
+  private static final String TRANSITIONTYPELINE = "            m->m     m->i     m->d     i->m     i->i     d->m     d->d";
+
+  private static String NL = System.lineSeparator();
+
+  private HiddenMarkovModel hmm;
+
+  // number of symbols in the alphabet used in the hidden Markov model
+  private int numberOfSymbols;
+
+  /**
+   * Constructor that parses immediately
+   * 
+   * @param inFile
+   * @param type
+   * @throws IOException
+   */
+  public HMMFile(String inFile, DataSourceType type) throws IOException
+  {
+    super(inFile, type);
+  }
+
+  /**
+   * Constructor that parses immediately
+   * 
+   * @param source
+   * @throws IOException
+   */
+  public HMMFile(FileParse source) throws IOException
+  {
+    super(source);
+  }
+
+  /**
+   * Default constructor
+   */
+  public HMMFile()
+  {
+  }
+
+  /**
+   * Constructor for HMMFile used for exporting
+   * 
+   * @param hmm
+   * @param exportImmediately
+   */
+  public HMMFile(HiddenMarkovModel markov)
+  {
+    hmm = markov;
+  }
+
+  /**
+   * Returns the HMM produced by parsing a HMMER3 file
+   * 
+   * @return
+   */
+  public HiddenMarkovModel getHMM()
+  {
+    return hmm;
+  }
+
+  /**
+   * Gets the name of the hidden Markov model
+   * 
+   * @return
+   */
+  public String getName()
+  {
+    return hmm.getName();
+  }
+
+  /**
+   * Reads the data from HMM file into the HMM model
+   */
+  @Override
+  public void parse()
+  {
+    try
+    {
+      hmm = new HiddenMarkovModel();
+      parseHeaderLines(dataIn);
+      parseModel(dataIn);
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+  }
+
+  /**
+   * Reads the header properties from a HMMER3 file and saves them in the
+   * HiddeMarkovModel. This method exits after reading the next line after the
+   * HMM line.
+   * 
+   * @param input
+   * @throws IOException
+   */
+  void parseHeaderLines(BufferedReader input) throws IOException
+  {
+    boolean readingHeaders = true;
+    hmm.setFileHeader(input.readLine());
+    String line = input.readLine();
+    while (readingHeaders && line != null)
+    {
+      Scanner parser = new Scanner(line);
+      String next = parser.next();
+      if (ALPHABET.equals(next))
+      {
+        String alphabetType = parser.next();
+        hmm.setProperty(ALPHABET, alphabetType);
+        String alphabet = ALPH_DNA.equalsIgnoreCase(alphabetType)
+                ? ALPHABET_DNA
+                : (ALPH_RNA.equalsIgnoreCase(alphabetType) ? ALPHABET_RNA
+                        : ALPHABET_AMINO);
+        numberOfSymbols = hmm.setAlphabet(alphabet);
+      }
+      else if (HMM.equals(next))
+      {
+        readingHeaders = false;
+        String symbols = line.substring(line.indexOf(HMM) + HMM.length());
+        numberOfSymbols = hmm.setAlphabet(symbols);
+      }
+      else if (STATISTICS.equals(next))
+      {
+        parser.next();
+        String key;
+        String value;
+        key = parser.next();
+        value = parser.next() + SPACE + SPACE + parser.next();
+        hmm.setProperty(key, value);
+      }
+      else
+      {
+        String key = next;
+        String value = parser.next();
+        while (parser.hasNext())
+        {
+          value = value + SPACE + parser.next();
+        }
+        hmm.setProperty(key, value);
+      }
+      parser.close();
+      line = input.readLine();
+    }
+  }
+
+  /**
+   * Parses the model data from the HMMER3 file. The input buffer should be
+   * positioned at the (optional) COMPO line if there is one, else at the insert
+   * emissions line for the BEGIN node of the model.
+   * 
+   * @param input
+   * @throws IOException
+   */
+  void parseModel(BufferedReader input) throws IOException
+  {
+    /*
+     * specification says there must always be an HMM header (already read)
+     * and one more header (guide headings) which is skipped here
+     */
+    int nodeNo = 0;
+    String line = input.readLine();
+    List<HMMNode> nodes = new ArrayList<>();
+
+    while (line != null && !TERMINATOR.equals(line))
+    {
+      HMMNode node = new HMMNode();
+      nodes.add(node);
+      Scanner scanner = new Scanner(line);
+      String next = scanner.next();
+
+      /*
+       * expect COMPO (optional) for average match emissions
+       * or a node number followed by node's match emissions
+       */
+      if (COMPO.equals(next) || nodeNo > 0)
+      {
+        /*
+         * parse match emissions
+         */
+        double[] matches = parseDoubles(scanner, numberOfSymbols);
+        node.setMatchEmissions(matches);
+        if (!COMPO.equals(next))
+        {
+          int resNo = parseAnnotations(scanner, node);
+          if (resNo == 0)
+          {
+            /*
+             * no MAP annotation provided, just number off from 0 (begin node)
+             */
+            resNo = nodeNo;
+          }
+          node.setResidueNumber(resNo);
+        }
+        line = input.readLine();
+      }
+      scanner.close();
+
+      /*
+       * parse insert emissions
+       */
+      scanner = new Scanner(line);
+      double[] inserts = parseDoubles(scanner, numberOfSymbols);
+      node.setInsertEmissions(inserts);
+      scanner.close();
+
+      /*
+       * parse state transitions
+       */
+      line = input.readLine();
+      scanner = new Scanner(line);
+      double[] transitions = parseDoubles(scanner,
+              NUMBER_OF_TRANSITIONS);
+      node.setStateTransitions(transitions);
+      scanner.close();
+      line = input.readLine();
+
+      nodeNo++;
+    }
+
+    hmm.setNodes(nodes);
+  }
+
+  /**
+   * Parses the annotations on the match emission line and add them to the node.
+   * (See p109 of the HMMER User Guide (V3.1b2) for the specification.) Returns
+   * the residue position that the node maps to, if provided, else zero.
+   * 
+   * @param scanner
+   * @param node
+   */
+  int parseAnnotations(Scanner scanner, HMMNode node)
+  {
+    int mapTo = 0;
+
+    /*
+     * map from hmm node to sequence position, if provided
+     */
+    if (scanner.hasNext())
+    {
+      String value = scanner.next();
+      if (!"-".equals(value))
+      {
+        try
+        {
+          mapTo = Integer.parseInt(value);
+          node.setResidueNumber(mapTo);
+        } catch (NumberFormatException e)
+        {
+          // ignore
+        }
+      }
+    }
+
+    /*
+     * hmm consensus residue if provided, else '-'
+     */
+    if (scanner.hasNext())
+    {
+      node.setConsensusResidue(scanner.next().charAt(0));
+    }
+
+    /*
+     * RF reference annotation, if provided, else '-'
+     */
+    if (scanner.hasNext())
+    {
+      node.setReferenceAnnotation(scanner.next().charAt(0));
+    }
+
+    /*
+     * 'm' for masked position, if provided, else '-'
+     */
+    if (scanner.hasNext())
+    {
+      node.setMaskValue(scanner.next().charAt(0));
+    }
+
+    /*
+     * structure consensus symbol, if provided, else '-'
+     */
+    if (scanner.hasNext())
+    {
+      node.setConsensusStructure(scanner.next().charAt(0));
+    }
+
+    return mapTo;
+  }
+
+  /**
+   * Fills an array of doubles parsed from an input line
+   * 
+   * @param input
+   * @param numberOfElements
+   * @return
+   * @throws IOException
+   */
+  static double[] parseDoubles(Scanner input,
+          int numberOfElements) throws IOException
+  {
+    double[] values = new double[numberOfElements];
+    for (int i = 0; i < numberOfElements; i++)
+    {
+      if (!input.hasNext())
+      {
+        throw new IOException("Incomplete data");
+      }
+      String next = input.next();
+      if (next.contains("*"))
+      {
+        values[i] = Double.NEGATIVE_INFINITY;
+      }
+      else
+      {
+        double prob = Double.valueOf(next);
+        prob = Math.pow(Math.E, -prob);
+        values[i] = prob;
+      }
+    }
+    return values;
+  }
+
+  /**
+   * Returns a string to be added to the StringBuilder containing the entire
+   * output String.
+   * 
+   * @param initialColumnSeparation
+   *          The initial whitespace separation between the left side of the
+   *          file and first character.
+   * @param columnSeparation
+   *          The separation between subsequent data entries.
+   * @param data
+   *          The list of data to be added to the String.
+   * @return
+   */
+  String addData(int initialColumnSeparation,
+          int columnSeparation, List<String> data)
+  {
+    String line = "";
+    boolean first = true;
+    for (String value : data)
+    {
+      int sep = first ? initialColumnSeparation : columnSeparation;
+      line += String.format("%" + sep + "s", value);
+      first = false;
+    }
+    return line;
+  }
+
+  /**
+   * Converts list of characters into a list of Strings.
+   * 
+   * @param list
+   * @return Returns the list of Strings.
+   */
+  List<String> charListToStringList(List<Character> list)
+  {
+    List<String> strList = new ArrayList<>();
+    for (char value : list)
+    {
+      String strValue = Character.toString(value);
+      strList.add(strValue);
+    }
+    return strList;
+  }
+
+  /**
+   * Converts an array of doubles into a list of Strings, rounded to the nearest
+   * 5th decimal place
+   * 
+   * @param doubles
+   * @param noOfDecimals
+   * @return
+   */
+  List<String> doublesToStringList(double[] doubles)
+  {
+    List<String> strList = new ArrayList<>();
+    for (double value : doubles)
+    {
+      String strValue;
+      if (value > 0)
+      {
+        strValue = String.format("%.5f", value);
+      }
+      else if (value == -0.00000d)
+      {
+        strValue = "0.00000";
+      }
+      else
+      {
+        strValue = "*";
+      }
+      strList.add(strValue);
+    }
+    return strList;
+  }
+
+  /**
+   * Appends model data in string format to the string builder
+   * 
+   * @param output
+   */
+  void appendModelAsString(StringBuilder output)
+  {
+    output.append(HMM).append("  ");
+    String charSymbols = hmm.getSymbols();
+    for (char c : charSymbols.toCharArray())
+    {
+      output.append(String.format("%9s", c));
+    }
+    output.append(NL).append(TRANSITIONTYPELINE);
+
+    int length = hmm.getLength();
+
+    for (int nodeNo = 0; nodeNo <= length; nodeNo++)
+    {
+      String matchLine = String.format("%7s",
+              nodeNo == 0 ? COMPO : Integer.toString(nodeNo));
+
+      double[] doubleMatches = convertToLogSpace(
+              hmm.getNode(nodeNo).getMatchEmissions());
+      List<String> strMatches = doublesToStringList(doubleMatches);
+      matchLine += addData(10, 9, strMatches);
+
+      if (nodeNo != 0)
+      {
+        matchLine += SPACE + (hmm.getNodeMapPosition(nodeNo));
+        matchLine += SPACE + hmm.getConsensusResidue(nodeNo);
+        matchLine += SPACE + hmm.getReferenceAnnotation(nodeNo);
+        if (hmm.getFileHeader().contains("HMMER3/f"))
+        {
+          matchLine += SPACE + hmm.getMaskedValue(nodeNo);
+          matchLine += SPACE + hmm.getConsensusStructure(nodeNo);
+        }
+      }
+
+      output.append(NL).append(matchLine);
+      
+      String insertLine = "";
+
+      double[] doubleInserts = convertToLogSpace(
+              hmm.getNode(nodeNo).getInsertEmissions());
+      List<String> strInserts = doublesToStringList(doubleInserts);
+      insertLine += addData(17, 9, strInserts);
+
+      output.append(NL).append(insertLine);
+
+      String transitionLine = "";
+      double[] doubleTransitions = convertToLogSpace(
+              hmm.getNode(nodeNo).getStateTransitions());
+      List<String> strTransitions = doublesToStringList(
+              doubleTransitions);
+      transitionLine += addData(17, 9, strTransitions);
+
+      output.append(NL).append(transitionLine);
+    }
+  }
+
+  /**
+   * Appends formatted HMM file properties to the string builder
+   * 
+   * @param output
+   */
+  void appendProperties(StringBuilder output)
+  {
+    output.append(hmm.getFileHeader());
+
+    String format = "%n%-5s %1s";
+    appendProperty(output, format, NAME);
+    appendProperty(output, format, ACCESSION_NUMBER);
+    appendProperty(output, format, DESCRIPTION);
+    appendProperty(output, format, LENGTH);
+    appendProperty(output, format, MAX_LENGTH);
+    appendProperty(output, format, ALPHABET);
+    appendBooleanProperty(output, format, REFERENCE_ANNOTATION);
+    appendBooleanProperty(output, format, MASKED_VALUE);
+    appendBooleanProperty(output, format, CONSENSUS_RESIDUE);
+    appendBooleanProperty(output, format, CONSENSUS_STRUCTURE);
+    appendBooleanProperty(output, format, MAP);
+    appendProperty(output, format, DATE);
+    appendProperty(output, format, NUMBER_OF_SEQUENCES);
+    appendProperty(output, format, EFF_NUMBER_OF_SEQUENCES);
+    appendProperty(output, format, CHECK_SUM);
+    appendProperty(output, format, GATHERING_THRESHOLD);
+    appendProperty(output, format, TRUSTED_CUTOFF);
+    appendProperty(output, format, NOISE_CUTOFF);
+
+    if (hmm.getMSV() != null)
+    {
+      format = "%n%-19s %18s";
+      output.append(String.format(format, "STATS LOCAL MSV", hmm.getMSV()));
+
+      output.append(String.format(format, "STATS LOCAL VITERBI",
+              hmm.getViterbi()));
+
+      output.append(String.format(format, "STATS LOCAL FORWARD",
+              hmm.getForward()));
+    }
+  }
+
+  /**
+   * Appends 'yes' or 'no' for the given property, according to whether or not
+   * it is set in the HMM
+   * 
+   * @param output
+   * @param format
+   * @param propertyName
+   */
+  private void appendBooleanProperty(StringBuilder output, String format,
+          String propertyName)
+  {
+    boolean set = hmm.getBooleanProperty(propertyName);
+    output.append(String.format(format, propertyName,
+            set ? HiddenMarkovModel.YES : HiddenMarkovModel.NO));
+  }
+
+  /**
+   * Appends the value of the given property to the output, if not null
+   * 
+   * @param output
+   * @param format
+   * @param propertyName
+   */
+  private void appendProperty(StringBuilder output, String format,
+          String propertyName)
+  {
+    String value = hmm.getProperty(propertyName);
+    if (value != null)
+    {
+      output.append(String.format(format, propertyName, value));
+    }
+  }
+
+  @Override
+  public String print(SequenceI[] sequences, boolean jvsuffix)
+  {
+    if (sequences[0].getHMM() != null)
+    {
+      hmm = sequences[0].getHMM();
+    }
+    return print();
+  }
+
+  /**
+   * Prints the .hmm file to a String.
+   * 
+   * @return
+   */
+  public String print()
+  {
+    StringBuilder output = new StringBuilder();
+    appendProperties(output);
+    output.append(NL);
+    appendModelAsString(output);
+    output.append(NL).append(TERMINATOR).append(NL);
+    return output.toString();
+  }
+
+  /**
+   * Converts the probabilities contained in an array into log space
+   * 
+   * @param ds
+   */
+  double[] convertToLogSpace(double[] ds)
+  {
+    double[] converted = new double[ds.length];
+    for (int i = 0; i < ds.length; i++)
+    {
+      double prob = ds[i];
+      double logProb = -1 * Math.log(prob);
+
+      converted[i] = logProb;
+    }
+    return converted;
+  }
+
+  /**
+   * Returns the HMM sequence produced by reading a .hmm file.
+   */
+  @Override
+  public SequenceI[] getSeqsAsArray()
+  {
+    SequenceI hmmSeq = hmm.getConsensusSequence();
+    SequenceI[] seq = new SequenceI[1];
+    seq[0] = hmmSeq;
+    return seq;
+  }
+
+  @Override
+  public void setNewlineString(String newLine)
+  {
+    NL = newLine;
+  }
+
+  @Override
+  public void setExportSettings(AlignExportSettingI exportSettings)
+  {
+
+  }
+
+  @Override
+  public void configureForView(AlignmentViewPanel viewpanel)
+  {
+
+  }
+
+  @Override
+  public boolean hasWarningMessage()
+  {
+    return false;
+  }
+
+  @Override
+  public String getWarningMessage()
+  {
+    return "warning message";
+  }
+
+}
+
diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index ff959b0..ad5884c 100755
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -150,6 +150,11 @@ public class IdentifyFile
           reply = FileFormat.ScoreMatrix;
           break;
         }
+        if (data.startsWith("HMMER3"))
+        {
+          reply = FileFormat.HMMER3;
+          break;
+        }
         if (data.startsWith("H ") && !aaIndexHeaderRead)
         {
           aaIndexHeaderRead = true;
diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index f5b5177..58b171d 100644
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -28,6 +28,7 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
 import jalview.datamodel.Mapping;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
@@ -42,10 +43,12 @@ import java.io.FileReader;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Enumeration;
+import java.util.HashMap;
 import java.util.Hashtable;
 import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.Map.Entry;
 import java.util.Vector;
 
 import com.stevesoft.pat.Regex;
@@ -76,23 +79,48 @@ public class StockholmFile extends AlignFile
 {
   private static final String ANNOTATION = "annotation";
 
-  private static final Regex OPEN_PAREN = new Regex("(<|\\[)", "(");
+  private static final char UNDERSCORE = '_';
 
-  private static final Regex CLOSE_PAREN = new Regex("(>|\\])", ")");
+  // private static final Regex OPEN_PAREN = new Regex("(<|\\[)", "(");
+  // private static final Regex CLOSE_PAREN = new Regex("(>|\\])", ")");
 
   public static final Regex DETECT_BRACKETS = new Regex(
           "(<|>|\\[|\\]|\\(|\\)|\\{|\\})");
 
-  StringBuffer out; // output buffer
+  /*
+   * lookup table of Stockholm 'feature' (annotation) types
+   * see http://sonnhammer.sbc.su.se/Stockholm.html
+   */
+  private static Map<String, String> featureTypes = null;
+
+  static
+  {
+    featureTypes = new HashMap<>();
+    featureTypes.put("SS", "Secondary Structure");
+    featureTypes.put("SA", "Surface Accessibility");
+    featureTypes.put("TM", "transmembrane");
+    featureTypes.put("PP", "Posterior Probability");
+    featureTypes.put("LI", "ligand binding");
+    featureTypes.put("AS", "active site");
+    featureTypes.put("IN", "intron");
+    featureTypes.put("IR", "interacting residue");
+    featureTypes.put("AC", "accession");
+    featureTypes.put("OS", "organism");
+    featureTypes.put("CL", "class");
+    featureTypes.put("DE", "description");
+    featureTypes.put("DR", "reference");
+    featureTypes.put("LO", "look");
+    featureTypes.put("RF", "Reference Positions");
+  }
 
-  AlignmentI al;
+  private AlignmentI al;
 
   public StockholmFile()
   {
   }
 
   /**
-   * Creates a new StockholmFile object for output.
+   * Creates a new StockholmFile object for output
    */
   public StockholmFile(AlignmentI al)
   {
@@ -110,6 +138,47 @@ public class StockholmFile extends AlignFile
     super(source);
   }
 
+  /**
+   * Answers the readable description for a (case-sensitive) annotation type
+   * code, for example "Reference Positions" for "RF". Returns the type code if
+   * no description is found.
+   * 
+   * @param id
+   * @return
+   */
+  public static String typeToDescription(String id)
+  {
+    if (featureTypes.containsKey(id))
+    {
+      return featureTypes.get(id);
+    }
+    System.err.println(
+            "Warning : Unknown Stockholm annotation type code " + id);
+    return id;
+  }
+
+  /**
+   * Answers the annotation type code for a (non-case-sensitive) readable
+   * description, for example "RF" for "Reference Positions" (or null if not
+   * found)
+   * 
+   * @param description
+   * @return
+   */
+  public static String descriptionToType(String description)
+  {
+    for (Entry<String, String> entry : featureTypes.entrySet())
+    {
+      if (entry.getValue().equalsIgnoreCase(description))
+      {
+        return entry.getKey();
+      }
+    }
+    System.err.println(
+            "Warning : Unknown Stockholm annotation type: " + description);
+    return null;
+  }
+
   @Override
   public void initData()
   {
@@ -197,7 +266,7 @@ public class StockholmFile extends AlignFile
     String version;
     // String id;
     Hashtable seqAnn = new Hashtable(); // Sequence related annotations
-    LinkedHashMap<String, String> seqs = new LinkedHashMap<String, String>();
+    LinkedHashMap<String, String> seqs = new LinkedHashMap<>();
     Regex p, r, rend, s, x;
     // Temporary line for processing RNA annotation
     // String RNAannot = "";
@@ -219,7 +288,7 @@ public class StockholmFile extends AlignFile
       // logger.debug("Stockholm version: " + version);
     }
 
-    // We define some Regexes here that will be used regularily later
+    // We define some Regexes here that will be used regularly later
     rend = new Regex("^\\s*\\/\\/"); // Find the end of an alignment
     p = new Regex("(\\S+)\\/(\\d+)\\-(\\d+)"); // split sequence id in
     // id/from/to
@@ -232,7 +301,7 @@ public class StockholmFile extends AlignFile
     Regex closeparen = new Regex("(>|\\])", ")");
 
     // Detect if file is RNA by looking for bracket types
-    Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");
+    // Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");
 
     rend.optimize();
     p.optimize();
@@ -366,7 +435,7 @@ public class StockholmFile extends AlignFile
               Hashtable content = (Hashtable) features.remove(type);
 
               // add alignment annotation for this feature
-              String key = type2id(type);
+              String key = descriptionToType(type);
 
               /*
                * have we added annotation rows for this type ?
@@ -624,17 +693,18 @@ public class StockholmFile extends AlignFile
             }
 
             Hashtable content;
-            if (features.containsKey(this.id2type(type)))
+            if (features.containsKey(StockholmFile.typeToDescription(type)))
             {
               // logger.debug("Found content for " + this.id2type(type));
-              content = (Hashtable) features.get(this.id2type(type));
+              content = (Hashtable) features
+                      .get(StockholmFile.typeToDescription(type));
             }
             else
             {
               // logger.debug("Creating new content holder for " +
               // this.id2type(type));
               content = new Hashtable();
-              features.put(this.id2type(type), content);
+              features.put(StockholmFile.typeToDescription(type), content);
             }
             String ns = (String) content.get(ANNOTATION);
 
@@ -658,7 +728,7 @@ public class StockholmFile extends AlignFile
               strucAnn = new Hashtable();
             }
 
-            Vector<AlignmentAnnotation> newStruc = new Vector<AlignmentAnnotation>();
+            Vector<AlignmentAnnotation> newStruc = new Vector<>();
             parseAnnotationRow(newStruc, type, ns);
             for (AlignmentAnnotation alan : newStruc)
             {
@@ -710,7 +780,7 @@ public class StockholmFile extends AlignFile
   private void guessDatabaseFor(Sequence seqO, String dbr, String dbsource)
   {
     DBRefEntry dbrf = null;
-    List<DBRefEntry> dbrs = new ArrayList<DBRefEntry>();
+    List<DBRefEntry> dbrs = new ArrayList<>();
     String seqdb = "Unknown", sdbac = "" + dbr;
     int st = -1, en = -1, p;
     if ((st = sdbac.indexOf("/")) > -1)
@@ -809,10 +879,8 @@ public class StockholmFile extends AlignFile
           Vector<AlignmentAnnotation> annotation, String label,
           String annots)
   {
-    String convert1, convert2 = null;
-
-    // convert1 = OPEN_PAREN.replaceAll(annots);
-    // convert2 = CLOSE_PAREN.replaceAll(convert1);
+    // String convert1 = OPEN_PAREN.replaceAll(annots);
+    // String convert2 = CLOSE_PAREN.replaceAll(convert1);
     // annots = convert2;
 
     String type = label;
@@ -823,7 +891,7 @@ public class StockholmFile extends AlignFile
               : label;
     }
     boolean ss = false, posterior = false;
-    type = id2type(type);
+    type = typeToDescription(type);
     if (type.equalsIgnoreCase("secondary structure"))
     {
       ss = true;
@@ -837,6 +905,10 @@ public class StockholmFile extends AlignFile
     for (int i = 0; i < annots.length(); i++)
     {
       String pos = annots.substring(i, i + 1);
+      if (UNDERSCORE == pos.charAt(0))
+      {
+        pos = " ";
+      }
       Annotation ann;
       ann = new Annotation(pos, "", ' ', 0f); // 0f is 'valid' null - will not
       // be written out
@@ -918,143 +990,123 @@ public class StockholmFile extends AlignFile
   }
 
   @Override
-  public String print(SequenceI[] s, boolean jvSuffix)
+  public String print(final SequenceI[] sequences, boolean jvSuffix)
   {
-    out = new StringBuffer();
+    StringBuilder out = new StringBuilder();
     out.append("# STOCKHOLM 1.0");
     out.append(newline);
 
-    // find max length of id
-    int max = 0;
-    int maxid = 0;
-    int in = 0;
-    Hashtable dataRef = null;
-    while ((in < s.length) && (s[in] != null))
+    int maxIdWidth = 0;
+    for (SequenceI seq : sequences)
     {
-      String tmp = printId(s[in], jvSuffix);
-      max = Math.max(max, s[in].getLength());
-
-      if (tmp.length() > maxid)
-      {
-        maxid = tmp.length();
-      }
-      if (s[in].getDBRefs() != null)
+      if (seq != null)
       {
-        for (int idb = 0; idb < s[in].getDBRefs().length; idb++)
-        {
-          if (dataRef == null)
-          {
-            dataRef = new Hashtable();
-          }
-
-          String datAs1 = s[in].getDBRefs()[idb].getSource().toString()
-                  + " ; "
-                  + s[in].getDBRefs()[idb].getAccessionId().toString();
-          dataRef.put(tmp, datAs1);
-        }
+        String formattedId = printId(seq, jvSuffix);
+        maxIdWidth = Math.max(maxIdWidth, formattedId.length());
       }
-      in++;
     }
-    maxid += 9;
-    int i = 0;
+    maxIdWidth += 9;
 
-    // output database type
-    if (al.getProperties() != null)
+    /*
+     * generic alignment properties
+     */
+    Hashtable props = al.getProperties();
+    if (props != null)
     {
-      if (!al.getProperties().isEmpty())
+      for (Object key : props.keySet())
       {
-        Enumeration key = al.getProperties().keys();
-        Enumeration val = al.getProperties().elements();
-        while (key.hasMoreElements())
-        {
-          out.append("#=GF " + key.nextElement() + " " + val.nextElement());
-          out.append(newline);
-        }
+        out.append(String.format("#=GF %s %s", key.toString(),
+                props.get(key).toString()));
+        out.append(newline);
       }
     }
 
-    // output database accessions
-    if (dataRef != null)
+    /*
+     * output database accessions as #=GS (per sequence annotation)
+     * PFAM or RFAM are output as AC <accession number>
+     * others are output as DR <dbname> ; <accession>
+     */
+    Format formatter = new Format("%-" + (maxIdWidth - 2) + "s");
+    for (SequenceI seq : sequences)
     {
-      Enumeration en = dataRef.keys();
-      while (en.hasMoreElements())
+      if (seq != null)
       {
-        Object idd = en.nextElement();
-        String type = (String) dataRef.remove(idd);
-        out.append(new Format("%-" + (maxid - 2) + "s")
-                .form("#=GS " + idd.toString() + " "));
-        if (type.contains("PFAM") || type.contains("RFAM"))
-        {
-
-          out.append(" AC " + type.substring(type.indexOf(";") + 1));
-        }
-        else
+        DBRefEntry[] dbRefs = seq.getDBRefs();
+        if (dbRefs != null)
         {
-          out.append(" DR " + type + " ");
+          String idField = formatter
+                  .form("#=GS " + printId(seq, jvSuffix) + " ");
+          for (DBRefEntry dbRef : dbRefs)
+          {
+            out.append(idField);
+            printDbRef(out, dbRef);
+          }
         }
-        out.append(newline);
       }
     }
 
-    // output annotations
-    while (i < s.length && s[i] != null)
+    /*
+     * output annotations
+     */
+    for (SequenceI seq : sequences)
     {
-      AlignmentAnnotation[] alAnot = s[i].getAnnotation();
-      if (alAnot != null)
+      if (seq != null)
       {
-        Annotation[] ann;
-        for (int j = 0; j < alAnot.length; j++)
+        AlignmentAnnotation[] alAnot = seq.getAnnotation();
+        if (alAnot != null)
         {
-
-          String key = type2id(alAnot[j].label);
-          boolean isrna = alAnot[j].isValidStruc();
-
-          if (isrna)
-          {
-            // hardwire to secondary structure if there is RNA secondary
-            // structure on the annotation
-            key = "SS";
-          }
-          if (key == null)
+          for (int j = 0; j < alAnot.length; j++)
           {
+            AlignmentAnnotation ann = alAnot[j];
+            String key = descriptionToType(ann.label);
+            boolean isrna = ann.isValidStruc();
+            if (isrna)
+            {
+              /*
+               * output as secondary structure if there is 
+               * RNA secondary structure on the annotation
+               */
+              key = "SS";
+            }
+            if (key == null)
+            {
+              continue;
+            }
 
-            continue;
-          }
-
-          // out.append("#=GR ");
-          out.append(new Format("%-" + maxid + "s").form(
-                  "#=GR " + printId(s[i], jvSuffix) + " " + key + " "));
-          ann = alAnot[j].annotations;
-          String seq = "";
-          for (int k = 0; k < ann.length; k++)
-          {
-            seq += outputCharacter(key, k, isrna, ann, s[i]);
+            out.append(new Format("%-" + maxIdWidth + "s").form(
+                    "#=GR " + printId(seq, jvSuffix) + " " + key + " "));
+            Annotation[] anns = ann.annotations;
+            StringBuilder seqString = new StringBuilder();
+            for (int k = 0; k < anns.length; k++)
+            {
+              seqString
+                      .append(getAnnotationCharacter(key, k, anns[k], seq));
+            }
+            out.append(seqString.toString());
+            out.append(newline);
           }
-          out.append(seq);
-          out.append(newline);
         }
-      }
 
-      out.append(new Format("%-" + maxid + "s")
-              .form(printId(s[i], jvSuffix) + " "));
-      out.append(s[i].getSequenceAsString());
-      out.append(newline);
-      i++;
+        out.append(new Format("%-" + maxIdWidth + "s")
+                .form(printId(seq, jvSuffix) + " "));
+        out.append(seq.getSequenceAsString());
+        out.append(newline);
+      }
     }
 
-    // alignment annotation
-    AlignmentAnnotation aa;
+    /*
+     * output alignment annotation (but not auto-calculated or sequence-related)
+     */
     if (al.getAlignmentAnnotation() != null)
     {
       for (int ia = 0; ia < al.getAlignmentAnnotation().length; ia++)
       {
-        aa = al.getAlignmentAnnotation()[ia];
+        AlignmentAnnotation aa = al.getAlignmentAnnotation()[ia];
         if (aa.autoCalculated || !aa.visible || aa.sequenceRef != null)
         {
           continue;
         }
-        String seq = "";
-        String label;
+        String label = aa.label;
         String key = "";
         if (aa.label.equals("seq"))
         {
@@ -1062,30 +1114,28 @@ public class StockholmFile extends AlignFile
         }
         else
         {
-          key = type2id(aa.label.toLowerCase());
-          if (key == null)
+          key = descriptionToType(aa.label);
+          if ("RF".equals(key))
           {
-            label = aa.label;
+            label = key;
           }
-          else
+          else if (key != null)
           {
             label = key + "_cons";
           }
         }
-        if (label == null)
-        {
-          label = aa.label;
-        }
         label = label.replace(" ", "_");
 
         out.append(
-                new Format("%-" + maxid + "s").form("#=GC " + label + " "));
-        boolean isrna = aa.isValidStruc();
+                new Format("%-" + maxIdWidth + "s")
+                        .form("#=GC " + label + " "));
+        StringBuilder sb = new StringBuilder(aa.annotations.length);
         for (int j = 0; j < aa.annotations.length; j++)
         {
-          seq += outputCharacter(key, j, isrna, aa.annotations, null);
+          sb.append(
+                  getAnnotationCharacter(key, j, aa.annotations[j], null));
         }
-        out.append(seq);
+        out.append(sb.toString());
         out.append(newline);
       }
     }
@@ -1097,20 +1147,40 @@ public class StockholmFile extends AlignFile
   }
 
   /**
-   * add an annotation character to the output row
+   * A helper method that appends a formatted dbref to the output buffer
+   * 
+   * @param out
+   * @param dbRef
+   */
+  protected void printDbRef(StringBuilder out, DBRefEntry dbRef)
+  {
+    String db = dbRef.getSource();
+    String acc = dbRef.getAccessionId();
+    if (DBRefSource.PFAM.equalsIgnoreCase(db)
+            || DBRefSource.RFAM.equalsIgnoreCase(db))
+    {
+      out.append(" AC " + acc);
+    }
+    else
+    {
+      out.append(" DR " + db + " ; " + acc);
+    }
+    out.append(newline);
+  }
+
+  /**
+   * Returns an annotation character to add to the output row
    * 
    * @param seq
    * @param key
    * @param k
-   * @param isrna
    * @param ann
    * @param sequenceI
    */
-  private char outputCharacter(String key, int k, boolean isrna,
-          Annotation[] ann, SequenceI sequenceI)
+  static char getAnnotationCharacter(String key, int k, Annotation annot,
+          SequenceI sequenceI)
   {
     char seq = ' ';
-    Annotation annot = ann[k];
     String ch = (annot == null)
             ? ((sequenceI == null) ? "-"
                     : Character.toString(sequenceI.getCharAt(k)))
@@ -1119,8 +1189,8 @@ public class StockholmFile extends AlignFile
     {
       if (annot == null)
       {
-        // sensible gap character
-        return ' ';
+        // Stockholm format requires underscore, not space
+        return UNDERSCORE;
       }
       else
       {
@@ -1147,77 +1217,6 @@ public class StockholmFile extends AlignFile
     return seq;
   }
 
-  public String print()
-  {
-    out = new StringBuffer();
-    out.append("# STOCKHOLM 1.0");
-    out.append(newline);
-    print(getSeqsAsArray(), false);
-
-    out.append("//");
-    out.append(newline);
-    return out.toString();
-  }
-
-  private static Hashtable typeIds = null;
-
-  static
-  {
-    if (typeIds == null)
-    {
-      typeIds = new Hashtable();
-      typeIds.put("SS", "Secondary Structure");
-      typeIds.put("SA", "Surface Accessibility");
-      typeIds.put("TM", "transmembrane");
-      typeIds.put("PP", "Posterior Probability");
-      typeIds.put("LI", "ligand binding");
-      typeIds.put("AS", "active site");
-      typeIds.put("IN", "intron");
-      typeIds.put("IR", "interacting residue");
-      typeIds.put("AC", "accession");
-      typeIds.put("OS", "organism");
-      typeIds.put("CL", "class");
-      typeIds.put("DE", "description");
-      typeIds.put("DR", "reference");
-      typeIds.put("LO", "look");
-      typeIds.put("RF", "Reference Positions");
-
-    }
-  }
-
-  protected static String id2type(String id)
-  {
-    if (typeIds.containsKey(id))
-    {
-      return (String) typeIds.get(id);
-    }
-    System.err.println(
-            "Warning : Unknown Stockholm annotation type code " + id);
-    return id;
-  }
-
-  protected static String type2id(String type)
-  {
-    String key = null;
-    Enumeration e = typeIds.keys();
-    while (e.hasMoreElements())
-    {
-      Object ll = e.nextElement();
-      if (typeIds.get(ll).toString().equalsIgnoreCase(type))
-      {
-        key = (String) ll;
-        break;
-      }
-    }
-    if (key != null)
-    {
-      return key;
-    }
-    System.err.println(
-            "Warning : Unknown Stockholm annotation type: " + type);
-    return key;
-  }
-
   /**
    * make a friendly ID string.
    * 
diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 1cf482d..8226cee 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -25,6 +25,8 @@ import jalview.api.SplitContainerI;
 import jalview.bin.Cache;
 import jalview.gui.JvSwingUtils;
 import jalview.gui.Preferences;
+import jalview.hmmer.HmmerCommand;
+import jalview.io.FileFormatException;
 import jalview.io.FileFormats;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
@@ -40,6 +42,7 @@ import java.awt.event.FocusEvent;
 import java.awt.event.KeyEvent;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
+import java.io.IOException;
 import java.util.HashMap;
 import java.util.Map;
 
@@ -67,6 +70,28 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenu webService = new JMenu();
 
+  protected JMenu hmmerMenu = new JMenu();
+
+  protected JMenu hmmAlign = new JMenu();
+
+  protected JMenuItem hmmAlignRun = new JMenuItem();
+
+  protected JMenuItem hmmAlignSettings = new JMenuItem();
+
+  protected JMenu hmmSearch = new JMenu();
+
+  protected JMenuItem hmmSearchRun = new JMenuItem();
+
+  protected JMenuItem hmmSearchSettings = new JMenuItem();
+
+  protected JMenuItem addDatabase = new JMenuItem();
+
+  protected JMenu hmmBuild = new JMenu();
+
+  protected JMenuItem hmmBuildRun = new JMenuItem();
+
+  protected JMenuItem hmmBuildSettings = new JMenuItem();
+
   protected JMenuItem webServiceNoServices;
 
   protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
@@ -195,13 +220,19 @@ public class GAlignFrame extends JInternalFrame
 
   protected JCheckBoxMenuItem normaliseSequenceLogo = new JCheckBoxMenuItem();
 
+  protected JCheckBoxMenuItem showInformationHistogram = new JCheckBoxMenuItem();
+
+  protected JCheckBoxMenuItem showHMMSequenceLogo = new JCheckBoxMenuItem();
+
+  protected JCheckBoxMenuItem normaliseHMMSequenceLogo = new JCheckBoxMenuItem();
+
   protected JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
 
   private SequenceAnnotationOrder annotationSortOrder;
 
   private boolean showAutoCalculatedAbove = false;
 
-  private Map<KeyStroke, JMenuItem> accelerators = new HashMap<KeyStroke, JMenuItem>();
+  private Map<KeyStroke, JMenuItem> accelerators = new HashMap<>();
 
   private SplitContainerI splitFrame;
 
@@ -249,7 +280,8 @@ public class GAlignFrame extends JInternalFrame
   private void jbInit() throws Exception
   {
     initColourMenu();
-
+    initHMMERMenu();
+  
     JMenuItem saveAs = new JMenuItem(
             MessageManager.getString("action.save_as"));
     ActionListener al = new ActionListener()
@@ -260,14 +292,14 @@ public class GAlignFrame extends JInternalFrame
         saveAs_actionPerformed(e);
       }
     };
-
+  
     // FIXME getDefaultToolkit throws an exception in Headless mode
     KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
                     | KeyEvent.SHIFT_MASK,
             false);
     addMenuActionAndAccelerator(keyStroke, saveAs, al);
-
+  
     closeMenuItem.setText(MessageManager.getString("action.close"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W,
             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
@@ -280,7 +312,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, closeMenuItem, al);
-
+  
     JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
     JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
     JMenu annotationsMenu = new JMenu(
@@ -290,6 +322,20 @@ public class GAlignFrame extends JInternalFrame
     JMenu calculateMenu = new JMenu(
             MessageManager.getString("action.calculate"));
     webService.setText(MessageManager.getString("action.web_service"));
+    hmmerMenu.setText(MessageManager.getString("action.hmmer"));
+    hmmerMenu.setEnabled(HmmerCommand.isHmmerAvailable());
+    hmmerMenu.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        hmmerMenu_actionPerformed(e);
+      }
+    });
+    hmmerMenu.add(hmmBuild);
+    hmmerMenu.add(hmmAlign);
+    hmmerMenu.add(hmmSearch);
+
     JMenuItem selectAllSequenceMenuItem = new JMenuItem(
             MessageManager.getString("action.select_all"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
@@ -303,7 +349,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, selectAllSequenceMenuItem, al);
-
+  
     JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
             MessageManager.getString("action.deselect_all"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0, false);
@@ -316,7 +362,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, deselectAllSequenceMenuItem, al);
-
+  
     JMenuItem invertSequenceMenuItem = new JMenuItem(
             MessageManager.getString("action.invert_sequence_selection"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
@@ -330,7 +376,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, invertSequenceMenuItem, al);
-
+  
     JMenuItem grpsFromSelection = new JMenuItem(
             MessageManager.getString("action.make_groups_selection"));
     grpsFromSelection.addActionListener(new ActionListener()
@@ -366,7 +412,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, remove2LeftMenuItem, al);
-
+  
     JMenuItem remove2RightMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_right"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
@@ -380,7 +426,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, remove2RightMenuItem, al);
-
+  
     JMenuItem removeGappedColumnMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_empty_columns"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
@@ -394,7 +440,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, removeGappedColumnMenuItem, al);
-
+  
     JMenuItem removeAllGapsMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_all_gaps"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
@@ -410,7 +456,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, removeAllGapsMenuItem, al);
-
+  
     JMenuItem justifyLeftMenuItem = new JMenuItem(
             MessageManager.getString("action.left_justify_alignment"));
     justifyLeftMenuItem.addActionListener(new ActionListener()
@@ -502,7 +548,7 @@ public class GAlignFrame extends JInternalFrame
         sortGroupMenuItem_actionPerformed(e);
       }
     });
-
+  
     JMenuItem removeRedundancyMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_redundancy"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
@@ -516,7 +562,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
-
+  
     JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
             MessageManager.getString("action.pairwise_alignment"));
     pairwiseAlignmentMenuItem.addActionListener(new ActionListener()
@@ -527,16 +573,18 @@ public class GAlignFrame extends JInternalFrame
         pairwiseAlignmentMenuItem_actionPerformed(e);
       }
     });
-
+  
     this.getContentPane().setLayout(new BorderLayout());
     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
     statusBar.setBackground(Color.white);
     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));
     statusBar.setText(MessageManager.getString("label.status_bar"));
+
     outputTextboxMenu
             .setText(MessageManager.getString("label.out_to_textbox"));
 
+
     annotationPanelMenuItem.setActionCommand("");
     annotationPanelMenuItem
             .setText(MessageManager.getString("label.show_annotations"));
@@ -604,6 +652,7 @@ public class GAlignFrame extends JInternalFrame
     final JCheckBoxMenuItem sortAnnByLabel = new JCheckBoxMenuItem(
             MessageManager.getString("label.sort_annotations_by_label"));
 
+
     sortAnnBySequence.setSelected(
             sortAnnotationsBy == SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
     sortAnnBySequence.addActionListener(new ActionListener()
@@ -644,7 +693,7 @@ public class GAlignFrame extends JInternalFrame
         colourTextMenuItem_actionPerformed(e);
       }
     });
-
+  
     JMenuItem htmlMenuItem = new JMenuItem(
             MessageManager.getString("label.html"));
     htmlMenuItem.addActionListener(new ActionListener()
@@ -655,7 +704,7 @@ public class GAlignFrame extends JInternalFrame
         htmlMenuItem_actionPerformed(e);
       }
     });
-
+  
     JMenuItem createBioJS = new JMenuItem(
             MessageManager.getString("label.biojs_html_export"));
     createBioJS.addActionListener(new java.awt.event.ActionListener()
@@ -666,7 +715,7 @@ public class GAlignFrame extends JInternalFrame
         bioJSMenuItem_actionPerformed(e);
       }
     });
-
+  
     JMenuItem overviewMenuItem = new JMenuItem(
             MessageManager.getString("label.overview_window"));
     overviewMenuItem.addActionListener(new ActionListener()
@@ -677,7 +726,7 @@ public class GAlignFrame extends JInternalFrame
         overviewMenuItem_actionPerformed(e);
       }
     });
-
+  
     undoMenuItem.setEnabled(false);
     undoMenuItem.setText(MessageManager.getString("action.undo"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
@@ -691,7 +740,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, undoMenuItem, al);
-
+  
     redoMenuItem.setEnabled(false);
     redoMenuItem.setText(MessageManager.getString("action.redo"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
@@ -705,7 +754,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
-
+  
     wrapMenuItem.setText(MessageManager.getString("label.wrap"));
     wrapMenuItem.addActionListener(new ActionListener()
     {
@@ -715,7 +764,7 @@ public class GAlignFrame extends JInternalFrame
         wrapMenuItem_actionPerformed(e);
       }
     });
-
+  
     JMenuItem printMenuItem = new JMenuItem(
             MessageManager.getString("action.print"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
@@ -729,7 +778,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, printMenuItem, al);
-
+  
     renderGapsMenuItem
             .setText(MessageManager.getString("action.show_gaps"));
     renderGapsMenuItem.setState(true);
@@ -741,7 +790,7 @@ public class GAlignFrame extends JInternalFrame
         renderGapsMenuItem_actionPerformed(e);
       }
     });
-
+  
     JMenuItem findMenuItem = new JMenuItem(
             MessageManager.getString("action.find"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
@@ -760,6 +809,7 @@ public class GAlignFrame extends JInternalFrame
 
     showSeqFeatures.setText(
             MessageManager.getString("label.show_sequence_features"));
+
     showSeqFeatures.addActionListener(new ActionListener()
     {
       @Override
@@ -778,86 +828,86 @@ public class GAlignFrame extends JInternalFrame
             .setText(MessageManager.getString("label.show_database_refs"));
     showDbRefsMenuitem.addActionListener(new ActionListener()
     {
-
+  
       @Override
       public void actionPerformed(ActionEvent e)
       {
         showDbRefs_actionPerformed(e);
       }
-
+  
     });
     showNpFeatsMenuitem.setText(
             MessageManager.getString("label.show_non_positional_features"));
     showNpFeatsMenuitem.addActionListener(new ActionListener()
     {
-
+  
       @Override
       public void actionPerformed(ActionEvent e)
       {
         showNpFeats_actionPerformed(e);
       }
-
+  
     });
     showGroupConservation
             .setText(MessageManager.getString("label.group_conservation"));
     showGroupConservation.addActionListener(new ActionListener()
     {
-
+  
       @Override
       public void actionPerformed(ActionEvent e)
       {
         showGroupConservation_actionPerformed(e);
       }
-
+  
     });
 
     showGroupConsensus
             .setText(MessageManager.getString("label.group_consensus"));
     showGroupConsensus.addActionListener(new ActionListener()
     {
-
+  
       @Override
       public void actionPerformed(ActionEvent e)
       {
         showGroupConsensus_actionPerformed(e);
       }
-
+  
     });
     showConsensusHistogram.setText(
             MessageManager.getString("label.show_consensus_histogram"));
     showConsensusHistogram.addActionListener(new ActionListener()
     {
-
+  
       @Override
       public void actionPerformed(ActionEvent e)
       {
         showConsensusHistogram_actionPerformed(e);
       }
-
+  
     });
     showSequenceLogo
             .setText(MessageManager.getString("label.show_consensus_logo"));
     showSequenceLogo.addActionListener(new ActionListener()
     {
-
+  
       @Override
       public void actionPerformed(ActionEvent e)
       {
         showSequenceLogo_actionPerformed(e);
       }
-
+  
     });
     normaliseSequenceLogo
             .setText(MessageManager.getString("label.norm_consensus_logo"));
     normaliseSequenceLogo.addActionListener(new ActionListener()
     {
-
+  
       @Override
       public void actionPerformed(ActionEvent e)
       {
         normaliseSequenceLogo_actionPerformed(e);
       }
-
+  
     });
     applyAutoAnnotationSettings
             .setText(MessageManager.getString("label.apply_all_groups"));
@@ -871,7 +921,7 @@ public class GAlignFrame extends JInternalFrame
         applyAutoAnnotationSettings_actionPerformed(e);
       }
     });
-
+  
     ButtonGroup buttonGroup = new ButtonGroup();
     final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
             MessageManager.getString("label.show_first"));
@@ -902,7 +952,7 @@ public class GAlignFrame extends JInternalFrame
         sortAnnotations_actionPerformed();
       }
     });
-
+  
     JMenuItem deleteGroups = new JMenuItem(
             MessageManager.getString("action.undefine_groups"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
@@ -916,7 +966,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
-
+  
     JMenuItem annotationColumn = new JMenuItem(
             MessageManager.getString("action.select_by_annotation"));
     annotationColumn.addActionListener(new ActionListener()
@@ -927,7 +977,7 @@ public class GAlignFrame extends JInternalFrame
         annotationColumn_actionPerformed(e);
       }
     });
-
+  
     JMenuItem createGroup = new JMenuItem(
             MessageManager.getString("action.create_group"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
@@ -941,7 +991,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, createGroup, al);
-
+  
     JMenuItem unGroup = new JMenuItem(
             MessageManager.getString("action.remove_group"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
@@ -957,7 +1007,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, unGroup, al);
-
+  
     copy.setText(MessageManager.getString("action.copy"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
@@ -971,7 +1021,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, copy, al);
-
+  
     cut.setText(MessageManager.getString("action.cut"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
@@ -984,7 +1034,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, cut, al);
-
+  
     JMenuItem delete = new JMenuItem(
             MessageManager.getString("action.delete"));
     delete.addActionListener(new ActionListener()
@@ -995,7 +1045,7 @@ public class GAlignFrame extends JInternalFrame
         delete_actionPerformed(e);
       }
     });
-
+  
     pasteMenu.setText(MessageManager.getString("action.paste"));
     JMenuItem pasteNew = new JMenuItem(
             MessageManager.getString("label.to_new_alignment"));
@@ -1008,11 +1058,18 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        pasteNew_actionPerformed(e);
+        try
+        {
+          pasteNew_actionPerformed(e);
+        } catch (IOException | InterruptedException e1)
+        {
+          // TODO Auto-generated catch block
+          e1.printStackTrace();
+        }
       }
     };
     addMenuActionAndAccelerator(keyStroke, pasteNew, al);
-
+  
     JMenuItem pasteThis = new JMenuItem(
             MessageManager.getString("label.to_this_alignment"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
@@ -1022,11 +1079,18 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        pasteThis_actionPerformed(e);
+        try
+        {
+          pasteThis_actionPerformed(e);
+        } catch (IOException | InterruptedException e1)
+        {
+          // TODO Auto-generated catch block
+          e1.printStackTrace();
+        }
       }
     };
     addMenuActionAndAccelerator(keyStroke, pasteThis, al);
-
+  
     JMenuItem createPNG = new JMenuItem("PNG");
     createPNG.addActionListener(new ActionListener()
     {
@@ -1038,7 +1102,6 @@ public class GAlignFrame extends JInternalFrame
     });
     createPNG.setActionCommand(
             MessageManager.getString("label.save_png_image"));
-
     JMenuItem font = new JMenuItem(MessageManager.getString("action.font"));
     font.addActionListener(new ActionListener()
     {
@@ -1068,7 +1131,7 @@ public class GAlignFrame extends JInternalFrame
         createEPS(null);
       }
     });
-
+  
     JMenuItem createSVG = new JMenuItem("SVG");
     createSVG.addActionListener(new ActionListener()
     {
@@ -1078,7 +1141,7 @@ public class GAlignFrame extends JInternalFrame
         createSVG(null);
       }
     });
-
+  
     JMenuItem loadTreeMenuItem = new JMenuItem(
             MessageManager.getString("label.load_associated_tree"));
     loadTreeMenuItem.setActionCommand(
@@ -1091,7 +1154,7 @@ public class GAlignFrame extends JInternalFrame
         loadTreeMenuItem_actionPerformed(e);
       }
     });
-
+  
     scaleAbove.setVisible(false);
     scaleAbove.setText(MessageManager.getString("action.scale_above"));
     scaleAbove.addActionListener(new ActionListener()
@@ -1142,15 +1205,15 @@ public class GAlignFrame extends JInternalFrame
             .setText(MessageManager.getString("label.automatic_scrolling"));
     followHighlightMenuItem.addActionListener(new ActionListener()
     {
-
+  
       @Override
       public void actionPerformed(ActionEvent e)
       {
         followHighlight_actionPerformed();
       }
-
+  
     });
-
+  
     sortByTreeMenu
             .setText(MessageManager.getString("action.by_tree_order"));
     sort.setText(MessageManager.getString("action.sort"));
@@ -1161,12 +1224,12 @@ public class GAlignFrame extends JInternalFrame
       {
         buildTreeSortMenu();
       }
-
+  
       @Override
       public void menuDeselected(MenuEvent e)
       {
       }
-
+  
       @Override
       public void menuCanceled(MenuEvent e)
       {
@@ -1177,17 +1240,17 @@ public class GAlignFrame extends JInternalFrame
     sort.add(sortByAnnotScore);
     sort.addMenuListener(new javax.swing.event.MenuListener()
     {
-
+  
       @Override
       public void menuCanceled(MenuEvent e)
       {
       }
-
+  
       @Override
       public void menuDeselected(MenuEvent e)
       {
       }
-
+  
       @Override
       public void menuSelected(MenuEvent e)
       {
@@ -1250,7 +1313,7 @@ public class GAlignFrame extends JInternalFrame
         showReverse_actionPerformed(true);
       }
     });
-
+  
     JMenuItem extractScores = new JMenuItem(
             MessageManager.getString("label.extract_scores"));
     extractScores.addActionListener(new ActionListener()
@@ -1263,10 +1326,10 @@ public class GAlignFrame extends JInternalFrame
     });
     extractScores.setVisible(true);
     // JBPNote: TODO: make gui for regex based score extraction
-
+  
     // for show products actions see AlignFrame.canShowProducts
     showProducts.setText(MessageManager.getString("label.get_cross_refs"));
-
+  
     runGroovy.setText(MessageManager.getString("label.run_groovy"));
     runGroovy.setToolTipText(
             MessageManager.getString("label.run_groovy_tip"));
@@ -1278,7 +1341,7 @@ public class GAlignFrame extends JInternalFrame
         runGroovy_actionPerformed();
       }
     });
-
+  
     JMenuItem openFeatureSettings = new JMenuItem(
             MessageManager.getString("action.feature_settings"));
     openFeatureSettings.addActionListener(new ActionListener()
@@ -1299,7 +1362,7 @@ public class GAlignFrame extends JInternalFrame
         fetchSequence_actionPerformed(e);
       }
     });
-
+  
     JMenuItem associatedData = new JMenuItem(
             MessageManager.getString("label.load_features_annotations"));
     associatedData.addActionListener(new ActionListener()
@@ -1307,7 +1370,14 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        associatedData_actionPerformed(e);
+        try
+        {
+          associatedData_actionPerformed(e);
+        } catch (IOException | InterruptedException e1)
+        {
+          // TODO Auto-generated catch block
+          e1.printStackTrace();
+        }
       }
     });
     loadVcf = new JMenuItem(MessageManager.getString("label.load_vcf_file"));
@@ -1361,7 +1431,7 @@ public class GAlignFrame extends JInternalFrame
         listenToViewSelections_actionPerformed(e);
       }
     });
-
+  
     JMenu addSequenceMenu = new JMenu(
             MessageManager.getString("label.add_sequences"));
     JMenuItem addFromFile = new JMenuItem(
@@ -1507,7 +1577,7 @@ public class GAlignFrame extends JInternalFrame
         hiddenMarkers_actionPerformed(e);
       }
     });
-
+  
     JMenuItem invertColSel = new JMenuItem(
             MessageManager.getString("action.invert_column_selection"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
@@ -1523,7 +1593,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, invertColSel, al);
-
+  
     showComplementMenuItem.setVisible(false);
     showComplementMenuItem.addActionListener(new ActionListener()
     {
@@ -1533,7 +1603,7 @@ public class GAlignFrame extends JInternalFrame
         showComplement_actionPerformed(showComplementMenuItem.getState());
       }
     });
-
+  
     tabbedPane.addChangeListener(new javax.swing.event.ChangeListener()
     {
       @Override
@@ -1554,7 +1624,7 @@ public class GAlignFrame extends JInternalFrame
           tabbedPane_mousePressed(e);
         }
       }
-
+  
       @Override
       public void mouseReleased(MouseEvent e)
       {
@@ -1572,7 +1642,7 @@ public class GAlignFrame extends JInternalFrame
         tabbedPane_focusGained(e);
       }
     });
-
+  
     JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
             Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
@@ -1585,7 +1655,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, save, al);
-
+  
     reload.setEnabled(false);
     reload.setText(MessageManager.getString("action.reload"));
     reload.addActionListener(new ActionListener()
@@ -1596,7 +1666,7 @@ public class GAlignFrame extends JInternalFrame
         reload_actionPerformed(e);
       }
     });
-
+  
     JMenuItem newView = new JMenuItem(
             MessageManager.getString("action.new_view"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
@@ -1610,11 +1680,11 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, newView, al);
-
+  
     tabbedPane.setToolTipText("<html><i>"
             + MessageManager.getString("label.rename_tab_eXpand_reGroup")
             + "</i></html>");
-
+  
     formatMenu.setText(MessageManager.getString("action.format"));
     JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
 
@@ -1628,7 +1698,7 @@ public class GAlignFrame extends JInternalFrame
         idRightAlign_actionPerformed(e);
       }
     });
-
+  
     gatherViews.setEnabled(false);
     gatherViews.setText(MessageManager.getString("action.gather_views"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
@@ -1641,7 +1711,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, gatherViews, al);
-
+  
     expandViews.setEnabled(false);
     expandViews.setText(MessageManager.getString("action.expand_views"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
@@ -1654,7 +1724,7 @@ public class GAlignFrame extends JInternalFrame
       }
     };
     addMenuActionAndAccelerator(keyStroke, expandViews, al);
-
+  
     JMenuItem pageSetup = new JMenuItem(
             MessageManager.getString("action.page_setup"));
     pageSetup.addActionListener(new ActionListener()
@@ -1687,12 +1757,87 @@ public class GAlignFrame extends JInternalFrame
         selectHighlightedColumns_actionPerformed(actionEvent);
       }
     };
+    hmmBuildRun.setText(MessageManager.formatMessage(
+            "label.action_with_default_settings", "hmmbuild"));
+    hmmBuildRun.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        hmmBuild_actionPerformed(true);
+      }
+    });
+    hmmBuildSettings.setText(
+            MessageManager.getString("label.edit_settings_and_run"));
+    hmmBuildSettings.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        hmmBuild_actionPerformed(false);
+      }
+    });
+    hmmAlignRun.setText(MessageManager.formatMessage(
+            "label.action_with_default_settings", "hmmalign"));
+    hmmAlignRun.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        hmmAlign_actionPerformed(true);
+      }
+    });
+    hmmAlignSettings.setText(
+            MessageManager.getString("label.edit_settings_and_run"));
+    hmmAlignSettings.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        hmmAlign_actionPerformed(false);
+      }
+    });
+    hmmSearchRun.setText(MessageManager.formatMessage(
+            "label.action_with_default_settings", "hmmsearch"));
+    hmmSearchRun.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        hmmSearch_actionPerformed(true);
+      }
+    });
+    hmmSearchSettings.setText(
+            MessageManager.getString("label.edit_settings_and_run"));
+    hmmSearchSettings.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        hmmSearch_actionPerformed(false);
+      }
+    });
+    addDatabase.setText(MessageManager.getString("label.add_database"));
+    addDatabase.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        try
+        {
+          addDatabase_actionPerformed();
+        } catch (IOException e1)
+        {
+          e1.printStackTrace();
+        }
+      }
+    });
     selectHighlighted.addActionListener(al);
     JMenu tooltipSettingsMenu = new JMenu(
             MessageManager.getString("label.sequence_id_tooltip"));
     JMenu autoAnnMenu = new JMenu(
             MessageManager.getString("label.autocalculated_annotation"));
-
+  
     JMenu exportImageMenu = new JMenu(
             MessageManager.getString("label.export_image"));
     JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
@@ -1705,7 +1850,8 @@ public class GAlignFrame extends JInternalFrame
     alignFrameMenuBar.add(colourMenu);
     alignFrameMenuBar.add(calculateMenu);
     alignFrameMenuBar.add(webService);
-
+    alignFrameMenuBar.add(hmmerMenu);
+  
     fileMenu.add(fetchSequence);
     fileMenu.add(addSequenceMenu);
     fileMenu.add(reload);
@@ -1725,7 +1871,7 @@ public class GAlignFrame extends JInternalFrame
     fileMenu.add(loadVcf);
     fileMenu.addSeparator();
     fileMenu.add(closeMenuItem);
-
+  
     pasteMenu.add(pasteNew);
     pasteMenu.add(pasteThis);
     editMenu.add(undoMenuItem);
@@ -1747,7 +1893,7 @@ public class GAlignFrame extends JInternalFrame
     // editMenu.add(justifyRightMenuItem);
     // editMenu.addSeparator();
     editMenu.add(padGapsMenuitem);
-
+  
     showMenu.add(showAllColumns);
     showMenu.add(showAllSeqs);
     showMenu.add(showAllhidden);
@@ -1775,7 +1921,7 @@ public class GAlignFrame extends JInternalFrame
     viewMenu.add(alignmentProperties);
     viewMenu.addSeparator();
     viewMenu.add(overviewMenuItem);
-
+  
     annotationsMenu.add(annotationPanelMenuItem);
     annotationsMenu.addSeparator();
     annotationsMenu.add(showAllAlAnnotations);
@@ -1819,7 +1965,7 @@ public class GAlignFrame extends JInternalFrame
     calculateMenu.add(extractScores);
     calculateMenu.addSeparator();
     calculateMenu.add(runGroovy);
-
+  
     webServiceNoServices = new JMenuItem(
             MessageManager.getString("label.no_services"));
     webService.add(webServiceNoServices);
@@ -1834,7 +1980,7 @@ public class GAlignFrame extends JInternalFrame
     this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
     statusPanel.add(statusBar, null);
     this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
-
+  
     formatMenu.add(font);
     formatMenu.addSeparator();
     formatMenu.add(wrapMenuItem);
@@ -1868,6 +2014,42 @@ public class GAlignFrame extends JInternalFrame
     // selectMenu.add(listenToViewSelections);
   }
 
+  public void hmmerMenu_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  /**
+   * Constructs the entries on the HMMER menu (does not add them to the menu).
+   */
+  protected void initHMMERMenu()
+  {
+    hmmAlign = new JMenu(MessageManager.getString("label.hmmalign"));
+    hmmAlignSettings = new JMenuItem(
+            MessageManager.getString("label.edit_settings_and_run"));
+    hmmAlignRun = new JMenuItem(MessageManager.formatMessage(
+            "label.action_with_default_settings", "hmmalign"));
+    hmmAlign.add(hmmAlignSettings);
+    hmmAlign.add(hmmAlignRun);
+    hmmBuild = new JMenu(MessageManager.getString("label.hmmbuild"));
+    hmmBuildSettings = new JMenuItem(
+            MessageManager.getString("label.edit_settings_and_run"));
+    hmmBuildRun = new JMenuItem(MessageManager.formatMessage(
+            "label.action_with_default_settings", "hmmbuild"));
+    hmmBuild.add(hmmBuildSettings);
+    hmmBuild.add(hmmBuildRun);
+    hmmSearch = new JMenu(MessageManager.getString("label.hmmsearch"));
+    hmmSearchSettings = new JMenuItem(
+            MessageManager.getString("label.edit_settings_and_run"));
+    hmmSearchRun = new JMenuItem(MessageManager.formatMessage(
+            "label.action_with_default_settings", "hmmsearch"));
+    addDatabase = new JMenuItem(
+            MessageManager.getString("label.add_database"));
+    hmmSearch.add(hmmSearchSettings);
+    hmmSearch.add(hmmSearchRun);
+    hmmSearch.add(addDatabase);
+  }
+
   protected void loadVcf_actionPerformed()
   {
   }
@@ -2343,10 +2525,12 @@ public class GAlignFrame extends JInternalFrame
   }
 
   protected void pasteNew_actionPerformed(ActionEvent e)
+          throws IOException, InterruptedException
   {
   }
 
   protected void pasteThis_actionPerformed(ActionEvent e)
+          throws IOException, InterruptedException
   {
   }
 
@@ -2354,6 +2538,23 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
+  protected void hmmBuild_actionPerformed(boolean withDefaults)
+  {
+  }
+
+  protected void hmmSearch_actionPerformed(boolean withDefaults)
+  {
+  }
+
+  protected void addDatabase_actionPerformed()
+          throws FileFormatException, IOException
+  {
+  }
+
+  protected void hmmAlign_actionPerformed(boolean withDefaults)
+  {
+  }
+
   public void createPNG(java.io.File f)
   {
   }
@@ -2469,6 +2670,7 @@ public class GAlignFrame extends JInternalFrame
   }
 
   public void associatedData_actionPerformed(ActionEvent e)
+          throws IOException, InterruptedException
   {
 
   }
diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index 1ca0802..358298d 100755
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -40,11 +40,11 @@ import java.awt.Insets;
 import java.awt.Rectangle;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
-import java.awt.event.FocusEvent;
 import java.awt.event.KeyEvent;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
 
+import javax.swing.AbstractButton;
 import javax.swing.AbstractCellEditor;
 import javax.swing.BorderFactory;
 import javax.swing.ButtonGroup;
@@ -142,10 +142,15 @@ public class GPreferences extends JPanel
 
   protected JCheckBox showConsensLogo = new JCheckBox();
 
+  protected JCheckBox showInformationHistogram = new JCheckBox();
+
+  protected JCheckBox showHMMLogo = new JCheckBox();
+
   protected JCheckBox showDbRefTooltip = new JCheckBox();
 
   protected JCheckBox showNpTooltip = new JCheckBox();
 
+
   /*
    * Structure tab and components
    */
@@ -265,6 +270,21 @@ public class GPreferences extends JPanel
   protected JCheckBox sortByTree = new JCheckBox();
 
   /*
+   * hmmer tab and components
+   */
+  protected JPanel hmmerTab = new JPanel();
+
+  protected JCheckBox hmmrTrimTermini = new JCheckBox();
+
+  protected AbstractButton hmmerBackgroundUniprot = new JCheckBox();
+
+  protected AbstractButton hmmerBackgroundAlignment = new JCheckBox();
+
+  protected JTextField hmmerSequenceCount = new JTextField();
+
+  protected JTextField hmmerPath = new JTextField();
+
+  /*
    * DAS Settings tab
    */
   protected JPanel dasTab = new JPanel();
@@ -274,6 +294,8 @@ public class GPreferences extends JPanel
    */
   protected JPanel wsTab = new JPanel();
 
+
+
   /**
    * Creates a new GPreferences object.
    */
@@ -325,6 +347,8 @@ public class GPreferences extends JPanel
     tabbedPane.add(initEditingTab(),
             MessageManager.getString("label.editing"));
 
+    tabbedPane.add(initHMMERTab(), MessageManager.getString("label.hmmer"));
+
     /*
      * See DasSourceBrowser for the real work of configuring this tab.
      */
@@ -339,7 +363,7 @@ public class GPreferences extends JPanel
 
     /*
      * Handler to validate a tab before leaving it - currently only for
-     * Structure.
+     * Structure
      */
     tabbedPane.addChangeListener(new ChangeListener()
     {
@@ -393,6 +417,83 @@ public class GPreferences extends JPanel
   }
 
   /**
+   * Initialises the hmmer tabbed panel
+   * 
+   * @return
+   */
+  private JPanel initHMMERTab()
+  {
+    hmmerTab.setLayout(null);
+
+    JLabel installationLocation = new JLabel(
+            MessageManager.getString("label.hmmer_location"));
+    installationLocation.setFont(LABEL_FONT);
+    installationLocation.setBounds(new Rectangle(22, 10, 250, 23));
+    hmmerPath.setBounds(new Rectangle(22, 30, 300, 23));
+    hmmerPath.addMouseListener(new MouseAdapter()
+    {
+      @Override
+      public void mouseClicked(MouseEvent e)
+      {
+        if (e.getClickCount() == 2)
+        {
+          String chosen = openFileChooser(true);
+          if (chosen != null)
+          {
+            hmmerPath.setText(chosen);
+          }
+        }
+      }
+    });
+
+    JLabel hmmalign = new JLabel(
+            MessageManager.getString("label.hmmalign_label"));
+    hmmalign.setFont(LABEL_FONT);
+    hmmalign.setBounds(new Rectangle(22, 50, 200, 23));
+
+    hmmrTrimTermini.setFont(LABEL_FONT);
+    hmmrTrimTermini.setText(MessageManager.getString("label.trim_termini"));
+    hmmrTrimTermini.setBounds(new Rectangle(22, 70, 200, 23));
+
+    JLabel hmmsearch = new JLabel(
+            MessageManager.getString("label.hmmsearch_label"));
+    hmmsearch.setFont(LABEL_FONT);
+    hmmsearch.setBounds(new Rectangle(22, 90, 200, 23));
+
+    JLabel sequencesToKeep = new JLabel(
+            MessageManager.getString("label.no_of_sequences"));
+    sequencesToKeep.setFont(LABEL_FONT);
+    sequencesToKeep.setBounds(new Rectangle(22, 110, 125, 23));
+    hmmerSequenceCount.setBounds(new Rectangle(150, 110, 40, 23));
+
+    ButtonGroup backgroundFreqSource = new ButtonGroup();
+    backgroundFreqSource.add(hmmerBackgroundUniprot);
+    backgroundFreqSource.add(hmmerBackgroundAlignment);
+    backgroundFreqSource.setSelected(hmmerBackgroundUniprot.getModel(), true);
+
+    hmmerBackgroundUniprot.setText(MessageManager.getString("label.freq_uniprot"));
+    hmmerBackgroundUniprot.setFont(LABEL_FONT);
+    hmmerBackgroundUniprot.setBounds(new Rectangle(22, 130, 255, 23));
+
+    hmmerBackgroundAlignment.setText(MessageManager.getString("label.freq_alignment"));
+    hmmerBackgroundAlignment.setFont(LABEL_FONT);
+    hmmerBackgroundAlignment.setBounds(new Rectangle(22, 150, 300, 23));
+
+    hmmerTab.add(hmmerBackgroundUniprot);
+    hmmerTab.add(hmmerBackgroundAlignment);
+    hmmerTab.add(hmmalign);
+    hmmerTab.add(hmmsearch);
+    hmmerTab.add(installationLocation);
+    hmmerTab.add(hmmerPath);
+    hmmerTab.add(hmmrTrimTermini);
+    hmmerTab.add(sequencesToKeep);
+    hmmerTab.add(sequencesToKeep);
+    hmmerTab.add(hmmerSequenceCount);
+
+    return hmmerTab;
+  }
+
+  /**
    * Initialises the Output tabbed panel.
    * 
    * @return
@@ -1222,7 +1323,7 @@ public class GPreferences extends JPanel
       {
         if (e.getClickCount() == 2)
         {
-          String chosen = openFileChooser();
+          String chosen = openFileChooser(false);
           if (chosen != null)
           {
             chimeraPath.setText(chosen);
@@ -1277,10 +1378,14 @@ public class GPreferences extends JPanel
    * 
    * @return
    */
-  protected String openFileChooser()
+  protected String openFileChooser(boolean forFolder)
   {
     String choice = null;
     JFileChooser chooser = new JFileChooser();
+    if (forFolder)
+    {
+      chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
+    }
 
     // chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(
@@ -1296,22 +1401,12 @@ public class GPreferences extends JPanel
     return choice;
   }
 
-  /**
-   * Validate the structure tab preferences; if invalid, set focus on this tab.
-   * 
-   * @param e
-   */
-  protected boolean validateStructure(FocusEvent e)
+  protected boolean validateStructure()
   {
-    if (!validateStructure())
-    {
-      e.getComponent().requestFocusInWindow();
-      return false;
-    }
-    return true;
+    return false;
   }
 
-  protected boolean validateStructure()
+  protected boolean validateHMMERPath(boolean showWarning)
   {
     return false;
   }
@@ -1819,4 +1914,9 @@ public class GPreferences extends JPanel
     }
 
   }
+
+  public void hmmerPath_actionPerformed(ActionEvent e)
+  {
+
+  }
 }
diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index 8a80d41..b2e569e 100644
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -29,12 +29,14 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.HiddenMarkovModel;
 import jalview.datamodel.ProfilesI;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.NucleotideColourScheme;
 import jalview.schemes.ResidueProperties;
 import jalview.schemes.ZappoColourScheme;
 import jalview.util.Platform;
+import jalview.workers.InformationThread;
 
 import java.awt.BasicStroke;
 import java.awt.Color;
@@ -70,8 +72,14 @@ public class AnnotationRenderer
 
   private final boolean MAC = Platform.isAMac();
 
-  boolean av_renderHistogram = true, av_renderProfile = true,
-          av_normaliseProfile = false;
+  // todo remove these flags, read from group/viewport where needed
+  boolean av_renderHistogram = true;
+
+  boolean av_renderProfile = true;
+
+  boolean av_normaliseProfile = false;
+
+  boolean av_infoHeight = false;
 
   ResidueShaderI profcolour = null;
 
@@ -87,6 +95,8 @@ public class AnnotationRenderer
 
   private boolean av_ignoreGapsConsensus;
 
+  private boolean av_ignoreBelowBackground;
+
   /**
    * attributes set from AwtRenderPanelI
    */
@@ -163,7 +173,7 @@ public class AnnotationRenderer
   {
     g.setColor(STEM_COLOUR);
     int sCol = (lastSSX / charWidth)
-            + hiddenColumns.adjustForHiddenColumns(startRes);
+            + hiddenColumns.visibleToAbsoluteColumn(startRes);
     int x1 = lastSSX;
     int x2 = (x * charWidth);
 
@@ -230,7 +240,7 @@ public class AnnotationRenderer
 
     g.setColor(nonCanColor);
     int sCol = (lastSSX / charWidth)
-            + hiddenColumns.adjustForHiddenColumns(startRes);
+            + hiddenColumns.visibleToAbsoluteColumn(startRes);
     int x1 = lastSSX;
     int x2 = (x * charWidth);
 
@@ -341,12 +351,16 @@ public class AnnotationRenderer
     }
     columnSelection = av.getColumnSelection();
     hiddenColumns = av.getAlignment().getHiddenColumns();
-    hconsensus = av.getSequenceConsensusHash();
+    hconsensus = av.getConsensusProfiles();
     complementConsensus = av.getComplementConsensusHash();
     hStrucConsensus = av.getRnaStructureConsensusHash();
     av_ignoreGapsConsensus = av.isIgnoreGapsConsensus();
+    av_ignoreBelowBackground = av.isIgnoreBelowBackground();
+    av_infoHeight = av.isInfoLetterHeight();
   }
 
+
+
   /**
    * Returns profile data; the first element is the profile type, the second is
    * the number of distinct values, the third the total count, and the remainder
@@ -362,17 +376,25 @@ public class AnnotationRenderer
     // properties/rendering attributes as a global 'alignment group' which holds
     // all vis settings for the alignment as a whole rather than a subset
     //
-    if (aa.autoCalculated && (aa.label.startsWith("Consensus")
-            || aa.label.startsWith("cDNA Consensus")))
+    if (InformationThread.HMM_CALC_ID.equals(aa.getCalcId()))
+    {
+      HiddenMarkovModel hmm = aa.sequenceRef.getHMM();
+      return AAFrequency.extractHMMProfile(hmm, column,
+              av_ignoreBelowBackground, av_infoHeight); // TODO check if this follows standard
+                                         // pipeline
+    }
+    if (aa.autoCalculated
+            && (aa.label.startsWith("Consensus") || aa.label
+                    .startsWith("cDNA Consensus")))
     {
       boolean forComplement = aa.label.startsWith("cDNA Consensus");
-      if (aa.groupRef != null && aa.groupRef.consensusData != null
+      if (aa.groupRef != null && aa.groupRef.getConsensusData() != null
               && aa.groupRef.isShowSequenceLogo())
       {
         // TODO? group consensus for cDNA complement
         return AAFrequency.extractProfile(
-                aa.groupRef.consensusData.get(column),
-                aa.groupRef.getIgnoreGapsConsensus());
+                aa.groupRef.getConsensusData().get(column),
+                aa.groupRef.isIgnoreGapsConsensus());
       }
       // TODO extend annotation row to enable dynamic and static profile data to
       // be stored
@@ -505,6 +527,21 @@ public class AnnotationRenderer
           renderProfile = av_renderProfile;
           normaliseProfile = av_normaliseProfile;
         }
+        else if (InformationThread.HMM_CALC_ID.equals(row.getCalcId()))
+        {
+          if (row.groupRef != null)
+          {
+            renderHistogram = row.groupRef.isShowInformationHistogram();
+            renderProfile = row.groupRef.isShowHMMSequenceLogo();
+            normaliseProfile = row.groupRef.isNormaliseHMMSequenceLogo();
+          }
+          else
+          {
+            renderHistogram = av.isShowInformationHistogram();
+            renderProfile = av.isShowHMMSequenceLogo();
+            normaliseProfile = av.isNormaliseHMMSequenceLogo();
+          }
+        }
         else
         {
           renderHistogram = true;
@@ -602,7 +639,7 @@ public class AnnotationRenderer
         {
           if (hasHiddenColumns)
           {
-            column = hiddenColumns.adjustForHiddenColumns(startRes + x);
+            column = hiddenColumns.visibleToAbsoluteColumn(startRes + x);
             if (column > row_annotations.length - 1)
             {
               break;
@@ -1150,7 +1187,7 @@ public class AnnotationRenderer
     g.setColor(HELIX_COLOUR);
 
     int sCol = (lastSSX / charWidth)
-            + hiddenColumns.adjustForHiddenColumns(startRes);
+            + hiddenColumns.visibleToAbsoluteColumn(startRes);
     int x1 = lastSSX;
     int x2 = (x * charWidth);
 
@@ -1250,7 +1287,7 @@ public class AnnotationRenderer
       column = sRes + x;
       if (hasHiddenColumns)
       {
-        column = hiddenColumns.adjustForHiddenColumns(column);
+        column = hiddenColumns.visibleToAbsoluteColumn(column);
       }
 
       if (column > aaMax)
@@ -1330,7 +1367,7 @@ public class AnnotationRenderer
       column = sRes + x;
       if (hasHiddenColumns)
       {
-        column = hiddenColumns.adjustForHiddenColumns(column);
+        column = hiddenColumns.visibleToAbsoluteColumn(column);
       }
 
       if (column > aaMax)
diff --git a/src/jalview/renderer/ResidueShaderI.java b/src/jalview/renderer/ResidueShaderI.java
index 4d97171..7e67598 100644
--- a/src/jalview/renderer/ResidueShaderI.java
+++ b/src/jalview/renderer/ResidueShaderI.java
@@ -5,16 +5,16 @@
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License 
+ * modify it under the terms of the GNU General License 
  * as published by the Free Software Foundation, either version 3
  * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
- * PURPOSE.  See the GNU General Public License for more details.
+ * PURPOSE.  See the GNU General License for more details.
  * 
- * You should have received a copy of the GNU General Public License
+ * You should have received a copy of the GNU General License
  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
@@ -32,16 +32,15 @@ import java.util.Map;
 
 public interface ResidueShaderI
 {
+  void setConsensus(ProfilesI cons);
 
-  public abstract void setConsensus(ProfilesI cons);
+  boolean conservationApplied();
 
-  public abstract boolean conservationApplied();
+  void setConservationApplied(boolean conservationApplied);
 
-  public abstract void setConservationApplied(boolean conservationApplied);
+  void setConservation(Conservation cons);
 
-  public abstract void setConservation(Conservation cons);
-
-  public abstract void alignmentChanged(AnnotatedCollectionI alignment,
+  void alignmentChanged(AnnotatedCollectionI alignment,
           Map<SequenceI, SequenceCollectionI> hiddenReps);
 
   /**
@@ -51,19 +50,19 @@ public interface ResidueShaderI
    * @param consensusThreshold
    * @param ignoreGaps
    */
-  public abstract void setThreshold(int consensusThreshold,
+  void setThreshold(int consensusThreshold,
           boolean ignoreGaps);
 
-  public abstract void setConservationInc(int i);
+  void setConservationInc(int i);
 
-  public abstract int getConservationInc();
+  int getConservationInc();
 
   /**
    * Get the percentage threshold for this colour scheme
    * 
    * @return Returns the percentage threshold
    */
-  public abstract int getThreshold();
+  int getThreshold();
 
   /**
    * Returns the possibly context dependent colour for the given symbol at the
@@ -75,11 +74,11 @@ public interface ResidueShaderI
    * @param seq
    * @return
    */
-  public abstract Color findColour(char symbol, int position,
+  Color findColour(char symbol, int position,
           SequenceI seq);
 
-  public abstract ColourSchemeI getColourScheme();
+  ColourSchemeI getColourScheme();
 
-  public abstract void setColourScheme(ColourSchemeI cs);
+  void setColourScheme(ColourSchemeI cs);
 
 }
\ No newline at end of file
diff --git a/src/jalview/renderer/ScaleRenderer.java b/src/jalview/renderer/ScaleRenderer.java
index d92608c..dc3272f 100644
--- a/src/jalview/renderer/ScaleRenderer.java
+++ b/src/jalview/renderer/ScaleRenderer.java
@@ -21,9 +21,11 @@
 package jalview.renderer;
 
 import jalview.api.AlignViewportI;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SequenceI;
 
 import java.util.ArrayList;
+import java.util.Iterator;
 import java.util.List;
 
 /**
@@ -60,27 +62,19 @@ public class ScaleRenderer
       column = col;
       text = txt;
     }
-
-    /**
-     * String representation for inspection when debugging only
-     */
-    @Override
-    public String toString()
-    {
-      return String.format("%s:%d:%s", major ? "major" : "minor", column,
-              text);
-    }
   }
 
   /**
-   * Calculates position markers on the alignment ruler
+   * calculate positions markers on the alignment ruler
    * 
    * @param av
    * @param startx
-   *          left-most column in visible view (0..)
+   *          left-most column in visible view
    * @param endx
-   *          - right-most column in visible view (0..)
-   * @return
+   *          - right-most column in visible view
+   * @return List of ScaleMark holding boolean: true/false for major/minor mark,
+   *         marker position in alignment column coords, a String to be rendered
+   *         at the position (or null)
    */
   public List<ScaleMark> calculateMarks(AlignViewportI av, int startx,
           int endx)
@@ -88,17 +82,27 @@ public class ScaleRenderer
     int scalestartx = (startx / 10) * 10;
 
     SequenceI refSeq = av.getAlignment().getSeqrep();
-    int refSp = 0, refStartI = 0, refEndI = -1;
+    int refSp = 0;
+    int refStartI = 0;
+    int refEndI = -1;
+
+    HiddenColumns hc = av.getAlignment().getHiddenColumns();
+
     if (refSeq != null)
     {
-      // find bounds and set origin appopriately
-      // locate first visible position for this sequence
-      int[] refbounds = av.getAlignment().getHiddenColumns()
-              .locateVisibleBoundsOfSequence(refSeq);
+      // find bounds and set origin appropriately
+      // locate first residue in sequence which is not hidden
+      Iterator<int[]> it = hc.iterator();
+      int index = refSeq.firstResidueOutsideIterator(it);
+      refSp = hc.absoluteToVisibleColumn(index);
+
+      refStartI = refSeq.findIndex(refSeq.getStart()) - 1;
+
+      int seqlength = refSeq.getLength();
+      // get sequence position past the end of the sequence
+      int pastEndPos = refSeq.findPosition(seqlength + 1);
+      refEndI = refSeq.findIndex(pastEndPos - 1) - 1;
 
-      refSp = refbounds[0];
-      refStartI = refbounds[4];
-      refEndI = refbounds[5];
       scalestartx = refSp + ((scalestartx - refSp) / 10) * 10;
     }
 
@@ -106,41 +110,40 @@ public class ScaleRenderer
     {
       scalestartx += 5;
     }
-    List<ScaleMark> marks = new ArrayList<ScaleMark>();
+    List<ScaleMark> marks = new ArrayList<>();
+    String string;
+    int refN, iadj;
     // todo: add a 'reference origin column' to set column number relative to
     for (int i = scalestartx; i <= endx; i += 5)
     {
       if (((i - refSp) % 10) == 0)
       {
-        String text;
         if (refSeq == null)
         {
-          int iadj = av.getAlignment().getHiddenColumns()
-                  .adjustForHiddenColumns(i - 1) + 1;
-          text = String.valueOf(iadj);
+          iadj = hc.visibleToAbsoluteColumn(i - 1) + 1;
+          string = String.valueOf(iadj);
         }
         else
         {
-          int iadj = av.getAlignment().getHiddenColumns()
-                  .adjustForHiddenColumns(i - 1);
-          int refN = refSeq.findPosition(iadj);
+          iadj = hc.visibleToAbsoluteColumn(i - 1);
+          refN = refSeq.findPosition(iadj);
           // TODO show bounds if position is a gap
           // - ie L--R -> "1L|2R" for
           // marker
           if (iadj < refStartI)
           {
-            text = String.valueOf(iadj - refStartI);
+            string = String.valueOf(iadj - refStartI);
           }
           else if (iadj > refEndI)
           {
-            text = "+" + String.valueOf(iadj - refEndI);
+            string = "+" + String.valueOf(iadj - refEndI);
           }
           else
           {
-            text = String.valueOf(refN) + refSeq.getCharAt(iadj);
+            string = String.valueOf(refN) + refSeq.getCharAt(iadj);
           }
         }
-        marks.add(new ScaleMark(true, i - startx - 1, text));
+        marks.add(new ScaleMark(true, i - startx - 1, string));
       }
       else
       {
diff --git a/src/jalview/schemes/HmmerColourScheme.java b/src/jalview/schemes/HmmerColourScheme.java
new file mode 100644
index 0000000..9ea468d
--- /dev/null
+++ b/src/jalview/schemes/HmmerColourScheme.java
@@ -0,0 +1,196 @@
+package jalview.schemes;
+
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.HiddenMarkovModel;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+import jalview.util.ColorUtils;
+import jalview.util.Comparison;
+
+import java.awt.Color;
+import java.util.Map;
+
+/**
+ * Base class for colour schemes based on a selected Hidden Markov Model. The
+ * colour is with reference to an HMM consensus sequence and HMM profile
+ * <ul>
+ * <li>white for a gap</li>
+ * <li>red for an insertion (position is gapped in the HMM consensus)</li>
+ * <li>orange for negative information content</li>
+ * <li>white to blue for increasing information content</li>
+ * </ul>
+ * where information content is the log ratio
+ * 
+ * <pre>
+ *   log(profile match emission probability / residue background probability)
+ * </pre>
+ * 
+ * Sub-class implementations use either global ('Uniprot') or local
+ * ('alignment') background frequencies.
+ * 
+ * @author tzvanaalten
+ * @author gmcarstairs
+ */
+public abstract class HmmerColourScheme extends ResidueColourScheme
+{
+  private static final Color INSERTION_COLOUR = new Color(230, 0, 0); // reddish
+
+  /*
+   * the aligned HMM consensus sequence to use as reference for colouring
+   */
+  private SequenceI hmmSeq;
+
+  private HiddenMarkovModel hmm;
+
+  private Map<Character, Float> frequencies;
+
+  /**
+   * Constructor given a Hidden Markov Model consensus sequence. This provides
+   * the HMM profile from which we can read the emission probabilities that
+   * determine the colour.
+   * 
+   * @param consensusSeq
+   */
+  public HmmerColourScheme(SequenceI consensusSeq)
+  {
+    hmmSeq = consensusSeq;
+    hmm = hmmSeq == null ? null : hmmSeq.getHMM();
+  }
+
+  /**
+   * Default constructor (required by ColourSchemes.loadColourSchemes)
+   */
+  public HmmerColourScheme()
+  {
+  }
+
+  @Override
+  public Color findColour(char symbol, int column, SequenceI seq,
+          String consensusResidue, float pid)
+  {
+    return findColour(symbol, column);
+  }
+
+  /**
+   * Returns the colour at a particular symbol at a column in the alignment:
+   * <ul>
+   * <li>white for a gap</li>
+   * <li>red for an insertion</li>
+   * <li>orange for negative information content</li>
+   * <li>white to blue for increasing information content</li>
+   * </ul>
+   * 
+   * @param symbol
+   * @param column
+   * @return
+   */
+  private Color findColour(char symbol, int column)
+  {
+    if (getHmm() == null || Comparison.isGap(symbol))
+    {
+      return Color.white;
+    }
+    if (Comparison.isGap(hmmSeq.getCharAt(column)))
+    {
+      return INSERTION_COLOUR;
+    }
+    if (Character.isLowerCase(symbol))
+    {
+      symbol = Character.toUpperCase(symbol);
+    }
+
+    final double prob = getHmm().getMatchEmissionProbability(column,
+            symbol);
+
+    Float freq = 0f;
+
+    if (!frequencies.containsKey(symbol))
+    {
+      return Color.WHITE;
+    }
+    else
+    {
+      freq = frequencies.get(symbol);
+    }
+
+    /*
+     * Orange if match emission probability is less than background probability
+     */
+    double infoRatio = prob / freq.floatValue();
+    Color colour = Color.ORANGE;
+    if (infoRatio >= 1)
+    {
+      /*
+       * log-scale graduated shade of blue if prob is greater than background  
+       */
+      float infoLog = (float) Math.log(infoRatio);
+      colour = ColorUtils.getGraduatedColour(infoLog, 0, Color.WHITE,
+              getMaxInformationScore(), Color.blue);
+    }
+
+    return colour;
+  }
+
+  /**
+   * Answers the maximum possible value of information score (log ratio), for
+   * use in scaling a graduated colour range
+   * 
+   * @return
+   */
+  abstract float getMaxInformationScore();
+
+  /**
+   * Answers a new colour scheme instance based on the HMM of the first sequence
+   * in ac that has an HMM
+   */
+  @Override
+  public ColourSchemeI getInstance(AnnotatedCollectionI ac,
+          Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+  {
+    return newInstance(ac);
+  }
+
+  /**
+   * Answers a new instance of the colour scheme for the given HMM
+   * 
+   * @param ac
+   * @return
+   */
+  protected abstract HmmerColourScheme newInstance(AnnotatedCollectionI ac);
+
+  @Override
+  public boolean isSimple()
+  {
+    return false;
+  }
+
+  /**
+   * Answers true if the sequence collection has an HMM consensus sequence, else
+   * false
+   */
+  @Override
+  public boolean isApplicableTo(AnnotatedCollectionI ac)
+  {
+    return ac.getHmmConsensus() != null;
+  }
+
+  protected Map<Character, Float> getFrequencies()
+  {
+    return frequencies;
+  }
+
+  protected void setFrequencies(Map<Character, Float> frequencies)
+  {
+    this.frequencies = frequencies;
+  }
+
+  protected HiddenMarkovModel getHmm()
+  {
+    return hmm;
+  }
+
+  protected SequenceI getHmmSequence()
+  {
+    return hmmSeq;
+  }
+}
diff --git a/src/jalview/schemes/HmmerGlobalBackground.java b/src/jalview/schemes/HmmerGlobalBackground.java
new file mode 100644
index 0000000..d5508f1
--- /dev/null
+++ b/src/jalview/schemes/HmmerGlobalBackground.java
@@ -0,0 +1,60 @@
+package jalview.schemes;
+
+import jalview.datamodel.AnnotatedCollectionI;
+
+/**
+ * An HMM colour scheme that uses global ('Uniprot') background frequencies for
+ * residues
+ * 
+ * @author tzvanaalten
+ */
+public class HmmerGlobalBackground extends HmmerColourScheme
+{
+  /*
+   * The highest possible log ratio is when match emission probability in
+   * the HMM model is 1, and background (for W) is 0.0109 giving
+   * log(1/0.0109) = log(91.743) = 4.519
+   */
+  private static final float MAX_LOG_RATIO = 4.519f;
+
+  /**
+   * Constructor given a Hidden Markov Model
+   * 
+   * @param markov
+   */
+  public HmmerGlobalBackground(AnnotatedCollectionI ac)
+  {
+    super(ac.getHmmConsensus());
+    String alphabetType = getHmm() == null
+            ? ResidueProperties.ALPHABET_AMINO
+            : getHmm().getAlphabetType();
+    setFrequencies(
+            ResidueProperties.backgroundFrequencies.get(alphabetType));
+  }
+
+  /**
+   * Default constructor (required by ColourSchemes.loadColourSchemes)
+   */
+  public HmmerGlobalBackground()
+  {
+  }
+
+  @Override
+  public String getSchemeName()
+  {
+    return JalviewColourScheme.HMMERU.toString();
+  }
+
+  @Override
+  protected HmmerColourScheme newInstance(AnnotatedCollectionI ac)
+  {
+    return new HmmerGlobalBackground(ac);
+  }
+
+  @Override
+  float getMaxInformationScore()
+  {
+    return MAX_LOG_RATIO;
+  }
+
+}
diff --git a/src/jalview/schemes/HmmerLocalBackground.java b/src/jalview/schemes/HmmerLocalBackground.java
new file mode 100644
index 0000000..d7a5e65
--- /dev/null
+++ b/src/jalview/schemes/HmmerLocalBackground.java
@@ -0,0 +1,97 @@
+package jalview.schemes;
+
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.ResidueCount;
+import jalview.datamodel.SequenceI;
+
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+/**
+ * An HMM colour scheme that uses local (alignment or sub-group) background
+ * frequencies for residues
+ * 
+ * @author tzvanaalten
+ */
+public class HmmerLocalBackground extends HmmerColourScheme
+{
+  float logTotalCount;
+
+  /**
+   * Constructor given a Hidden Markov Model
+   * 
+   * @param sg
+   * 
+   * @param markov
+   */
+  public HmmerLocalBackground(AnnotatedCollectionI ac)
+  {
+    super(ac.getHmmConsensus());
+    countFrequencies(ac);
+  }
+
+  /**
+   * Default constructor (required by ColourSchemes.loadColourSchemes)
+   */
+  public HmmerLocalBackground()
+  {
+  }
+
+  @Override
+  public String getSchemeName()
+  {
+    return JalviewColourScheme.HMMERA.toString();
+  }
+
+  /**
+   * Counts and stores the relative frequency of every residue in the alignment
+   * (apart from any HMM consensus sequences)
+   * 
+   * @param sg
+   */
+  public void countFrequencies(AnnotatedCollectionI sg)
+  {
+    // TODO or total counts in Consensus Profile (how do we get at it?)?
+    Map<Character, Float> freqs = new HashMap<>();
+
+    /*
+     * count symbols, excluding any HMM consensus sequences
+     */
+    ResidueCount counts = new ResidueCount();
+    List<SequenceI> seqs = sg.getSequences();
+    for (SequenceI seq : seqs)
+    {
+      if (!seq.isHMMConsensusSequence())
+      {
+        for (char c : seq.getSequence())
+        {
+          counts.add(c);
+        }
+      }
+    }
+    int total = counts.getTotalResidueCount(); // excludes gaps
+
+    for (char symbol : counts.getSymbolCounts().symbols)
+    {
+      double freq = counts.getCount(symbol) / (double) total;
+      freqs.put(symbol, (float) freq);
+    }
+
+    setFrequencies(freqs);
+
+    logTotalCount = (float) Math.log(total);
+  }
+
+  @Override
+  float getMaxInformationScore()
+  {
+    return logTotalCount;
+  }
+
+  @Override
+  protected HmmerColourScheme newInstance(AnnotatedCollectionI ac)
+  {
+    return new HmmerLocalBackground(ac);
+  }
+}
diff --git a/src/jalview/schemes/JalviewColourScheme.java b/src/jalview/schemes/JalviewColourScheme.java
index e1fc02d..357ea03 100644
--- a/src/jalview/schemes/JalviewColourScheme.java
+++ b/src/jalview/schemes/JalviewColourScheme.java
@@ -42,7 +42,9 @@ public enum JalviewColourScheme
   Nucleotide("Nucleotide", NucleotideColourScheme.class),
   PurinePyrimidine("Purine/Pyrimidine", PurinePyrimidineColourScheme.class),
   RNAHelices("RNA Helices", RNAHelicesColour.class),
-  TCoffee("T-Coffee Scores", TCoffeeColourScheme.class);
+  TCoffee("T-Coffee Scores", TCoffeeColourScheme.class),
+  HMMERU("HMMER-Uniprot", HmmerGlobalBackground.class),
+  HMMERA("HMMER-Alignment", HmmerLocalBackground.class);
   // RNAInteraction("RNA Interaction type", RNAInteractionColourScheme.class)
 
   private String name;
diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index a4e6480..9b0489e 100755
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -32,6 +32,13 @@ import java.util.Vector;
 
 public class ResidueProperties
 {
+  // alphabet names used in Hidden Markov Model files
+  public static final String ALPHABET_RNA = "RNA";
+
+  public static final String ALPHABET_DNA = "DNA";
+
+  public static final String ALPHABET_AMINO = "amino";
+
   // Stores residue codes/names and colours and other things
   public static final int[] aaIndex; // aaHash version 2.1.1 and below
 
@@ -48,6 +55,9 @@ public class ResidueProperties
   // lookup from modified amino acid (e.g. MSE) to canonical form (e.g. MET)
   public static final Map<String, String> modifications = new HashMap<>();
 
+  // residue background frequencies across different alphabets
+  public static final Map<String, Map<Character, Float>> backgroundFrequencies = new HashMap<>();
+
   static
   {
     aaIndex = new int[255];
@@ -2517,6 +2527,58 @@ public class ResidueProperties
 
   }
 
+  static
+  {
+    Map<Character, Float> amino = new HashMap<>();
+    amino.put('A', 0.0826f);
+    amino.put('Q', 0.0393f);
+    amino.put('L', 0.0965f);
+    amino.put('S', 0.0661f);
+    amino.put('R', 0.0553f);
+    amino.put('E', 0.0674f);
+    amino.put('K', 0.0582f);
+    amino.put('T', 0.0535f);
+    amino.put('N', 0.0406f);
+    amino.put('G', 0.0708f);
+    amino.put('M', 0.0241f);
+    amino.put('W', 0.0109f);
+    amino.put('D', 0.0546f);
+    amino.put('H', 0.0227f);
+    amino.put('F', 0.0386f);
+    amino.put('Y', 0.0292f);
+    amino.put('C', 0.0137f);
+    amino.put('I', 0.0593f);
+    amino.put('P', 0.0472f);
+    amino.put('V', 0.0686f);
+    backgroundFrequencies.put(ALPHABET_AMINO, amino);
+    // todo: these don't match https://www.ebi.ac.uk/uniprot/TrEMBLstats - what
+    // are they?
+  }
+
+  // TODO get correct frequencies
+
+  static
+  {
+    Map<Character, Float> dna = new HashMap<>();
+    dna.put('A', 0.25f);
+    dna.put('C', 0.25f);
+    dna.put('T', 0.25f);
+    dna.put('G', 0.25f);
+    backgroundFrequencies.put(ALPHABET_DNA, dna);
+
+  }
+
+  static
+  {
+    Map<Character, Float> rna = new HashMap<>();
+    rna.put('A', 0.25f);
+    rna.put('C', 0.25f);
+    rna.put('T', 0.25f);
+    rna.put('G', 0.25f);
+    backgroundFrequencies.put(ALPHABET_RNA, rna);
+
+  }
+
   public static String getCanonicalAminoAcid(String aA)
   {
     String canonical = modifications.get(aA);
diff --git a/src/jalview/structure/StructureMapping.java b/src/jalview/structure/StructureMapping.java
index 40789ed..fcf322d 100644
--- a/src/jalview/structure/StructureMapping.java
+++ b/src/jalview/structure/StructureMapping.java
@@ -21,6 +21,7 @@
 package jalview.structure;
 
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Mapping;
 import jalview.datamodel.SequenceI;
 
 import java.util.ArrayList;
@@ -39,7 +40,7 @@ public class StructureMapping
 
   String pdbchain;
 
-  public static final int UNASSIGNED_VALUE = -1;
+  public static final int UNASSIGNED_VALUE = Integer.MIN_VALUE;
 
   private static final int PDB_RES_NUM_INDEX = 0;
 
@@ -49,6 +50,7 @@ public class StructureMapping
   // and atomNo
   HashMap<Integer, int[]> mapping;
 
+  jalview.datamodel.Mapping seqToPdbMapping = null;
   /**
    * Constructor
    * 
@@ -73,6 +75,14 @@ public class StructureMapping
     this.mappingDetails = mappingDetails;
   }
 
+  public StructureMapping(SequenceI seq, String pdbFile2, String pdbId2,
+          String chain, HashMap<Integer, int[]> mapping2,
+          String mappingOutput, Mapping seqToPdbMapping)
+  {
+    this(seq, pdbFile2, pdbId2, chain, mapping2, mappingOutput);
+    this.seqToPdbMapping = seqToPdbMapping;
+  }
+
   public SequenceI getSequence()
   {
     return sequence;
@@ -109,7 +119,8 @@ public class StructureMapping
   /**
    * 
    * @param seqpos
-   * @return 0 or the corresponding residue number for the sequence position
+   * @return UNASSIGNED_VALUE or the corresponding residue number for the
+   *         sequence position
    */
   public int getPDBResNum(int seqpos)
   {
@@ -247,4 +258,9 @@ public class StructureMapping
   {
     return mapping;
   }
+
+  public Mapping getSeqToPdbMapping()
+  {
+    return seqToPdbMapping;
+  }
 }
diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 35e2536..10fe836 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -74,8 +74,6 @@ public class StructureSelectionManager
 
   private boolean addTempFacAnnot = false;
 
-  private SiftsClient siftsClient = null;
-
   /*
    * Set of any registered mappings between (dataset) sequences.
    */
@@ -328,22 +326,20 @@ public class StructureSelectionManager
   }
 
   /**
-   * create sequence structure mappings between each sequence and the given
-   * pdbFile (retrieved via the given protocol).
+   * Import a single structure file and register sequence structure mappings for
+   * broadcasting colouring, mouseovers and selection events (convenience
+   * wrapper).
    * 
    * @param forStructureView
    *          when true, record the mapping for use in mouseOvers
-   * 
-   * @param sequenceArray
+   * @param sequence
    *          - one or more sequences to be mapped to pdbFile
-   * @param targetChainIds
+   * @param targetChains
    *          - optional chain specification for mapping each sequence to pdb
-   *          (may be nill, individual elements may be nill) - JBPNote: JAL-2693
-   *          - this should be List<List<String>>, empty lists indicate no
-   *          predefined mappings
+   *          (may be nill, individual elements may be nill)
    * @param pdbFile
    *          - structure data resource
-   * @param sourceType
+   * @param protocol
    *          - how to resolve data from resource
    * @return null or the structure data parsed as a pdb file
    */
@@ -355,46 +351,51 @@ public class StructureSelectionManager
             pdbFile, sourceType, null);
   }
 
+  /**
+   * create sequence structure mappings between each sequence and the given
+   * pdbFile (retrieved via the given protocol). Either constructs a mapping
+   * using NW alignment or derives one from any available SIFTS mapping data.
+   * 
+   * @param forStructureView
+   *          when true, record the mapping for use in mouseOvers
+   * 
+   * @param sequenceArray
+   *          - one or more sequences to be mapped to pdbFile
+   * @param targetChainIds
+   *          - optional chain specification for mapping each sequence to pdb
+   *          (may be nill, individual elements may be nill) - JBPNote: JAL-2693
+   *          - this should be List<List<String>>, empty lists indicate no
+   *          predefined mappings
+   * @param pdbFile
+   *          - structure data resource
+   * @param sourceType
+   *          - how to resolve data from resource
+   * @param IProgressIndicator
+   *          reference to UI component that maintains a progress bar for the
+   *          mapping operation
+   * @return null or the structure data parsed as a pdb file
+   */
   synchronized public StructureFile computeMapping(
           boolean forStructureView, SequenceI[] sequenceArray,
           String[] targetChainIds, String pdbFile, DataSourceType sourceType,
           IProgressIndicator progress)
   {
     long progressSessionId = System.currentTimeMillis() * 3;
-    /*
-     * There will be better ways of doing this in the future, for now we'll use
-     * the tried and tested MCview pdb mapping
+
+    /**
+     * do we extract and transfer annotation from 3D data ?
      */
-    boolean parseSecStr = processSecondaryStructure;
-    if (isPDBFileRegistered(pdbFile))
-    {
-      for (SequenceI sq : sequenceArray)
-      {
-        SequenceI ds = sq;
-        while (ds.getDatasetSequence() != null)
-        {
-          ds = ds.getDatasetSequence();
-        }
-        ;
-        if (ds.getAnnotation() != null)
-        {
-          for (AlignmentAnnotation ala : ds.getAnnotation())
-          {
-            // false if any annotation present from this structure
-            // JBPNote this fails for jmol/chimera view because the *file* is
-            // passed, not the structure data ID -
-            if (PDBfile.isCalcIdForFile(ala, findIdForPDBFile(pdbFile)))
-            {
-              parseSecStr = false;
-            }
-          }
-        }
-      }
-    }
+    // FIXME: possibly should just delete
+
+    boolean parseSecStr = processSecondaryStructure
+            ? isStructureFileProcessed(pdbFile, sequenceArray)
+            : false;
+
     StructureFile pdb = null;
     boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
     try
     {
+      // FIXME if sourceType is not null, we've lost data here
       sourceType = AppletFormatAdapter.checkProtocol(pdbFile);
       pdb = new JmolParser(pdbFile, sourceType);
 
@@ -411,7 +412,10 @@ public class StructureSelectionManager
       ex.printStackTrace();
       return null;
     }
-
+    /*
+     * sifts client - non null if SIFTS mappings are to be used 
+     */
+    SiftsClient siftsClient = null;
     try
     {
       if (isMapUsingSIFTs)
@@ -422,6 +426,7 @@ public class StructureSelectionManager
     {
       isMapUsingSIFTs = false;
       e.printStackTrace();
+      siftsClient = null;
     }
 
     String targetChainId;
@@ -524,12 +529,12 @@ public class StructureSelectionManager
           try
           {
             siftsMapping = getStructureMapping(seq, pdbFile, targetChainId,
-                    pdb, maxChain, sqmpping, maxAlignseq);
+                    pdb, maxChain, sqmpping, maxAlignseq, siftsClient);
             seqToStrucMapping.add(siftsMapping);
-            maxChain.makeExactMapping(maxAlignseq, seq);
-            maxChain.transferRESNUMFeatures(seq, null);// FIXME: is this
+            maxChain.makeExactMapping(siftsMapping, seq);
+            maxChain.transferRESNUMFeatures(seq, "IEA: SIFTS");// FIXME: is this
                                                        // "IEA:SIFTS" ?
-            maxChain.transferResidueAnnotation(siftsMapping, sqmpping);
+            maxChain.transferResidueAnnotation(siftsMapping, null);
             ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
 
           } catch (SiftsException e)
@@ -540,7 +545,8 @@ public class StructureSelectionManager
                     targetChainId, maxChain, pdb, maxAlignseq);
             seqToStrucMapping.add(nwMapping);
             maxChain.makeExactMapping(maxAlignseq, seq);
-            maxChain.transferRESNUMFeatures(seq, null); // FIXME: is this
+            maxChain.transferRESNUMFeatures(seq, "IEA:Jalview"); // FIXME: is
+                                                                 // this
                                                         // "IEA:Jalview" ?
             maxChain.transferResidueAnnotation(nwMapping, sqmpping);
             ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
@@ -551,11 +557,17 @@ public class StructureSelectionManager
           List<StructureMapping> foundSiftsMappings = new ArrayList<>();
           for (PDBChain chain : pdb.getChains())
           {
+            StructureMapping siftsMapping = null;
             try
             {
-              StructureMapping siftsMapping = getStructureMapping(seq,
-                      pdbFile, chain.id, pdb, chain, sqmpping, maxAlignseq);
+              siftsMapping = getStructureMapping(seq,
+                      pdbFile, chain.id, pdb, chain, sqmpping, maxAlignseq,
+                      siftsClient);
               foundSiftsMappings.add(siftsMapping);
+              chain.makeExactMapping(siftsMapping, seq);
+              chain.transferRESNUMFeatures(seq, "IEA: SIFTS");// FIXME: is this
+              // "IEA:SIFTS" ?
+              chain.transferResidueAnnotation(siftsMapping, null);
             } catch (SiftsException e)
             {
               System.err.println(e.getMessage());
@@ -564,11 +576,6 @@ public class StructureSelectionManager
           if (!foundSiftsMappings.isEmpty())
           {
             seqToStrucMapping.addAll(foundSiftsMappings);
-            maxChain.makeExactMapping(maxAlignseq, seq);
-            maxChain.transferRESNUMFeatures(seq, null);// FIXME: is this
-                                                       // "IEA:SIFTS" ?
-            maxChain.transferResidueAnnotation(foundSiftsMappings.get(0),
-                    sqmpping);
             ds.addPDBId(sqmpping.getTo().getAllPDBEntries().get(0));
           }
           else
@@ -608,6 +615,46 @@ public class StructureSelectionManager
     return pdb;
   }
 
+  /**
+   * check if we need to extract secondary structure from given pdbFile and
+   * transfer to sequences
+   * 
+   * @param pdbFile
+   * @param sequenceArray
+   * @return
+   */
+  private boolean isStructureFileProcessed(String pdbFile,
+          SequenceI[] sequenceArray)
+  {
+    boolean parseSecStr = true;
+    if (isPDBFileRegistered(pdbFile))
+    {
+      for (SequenceI sq : sequenceArray)
+      {
+        SequenceI ds = sq;
+        while (ds.getDatasetSequence() != null)
+        {
+          ds = ds.getDatasetSequence();
+        }
+        ;
+        if (ds.getAnnotation() != null)
+        {
+          for (AlignmentAnnotation ala : ds.getAnnotation())
+          {
+            // false if any annotation present from this structure
+            // JBPNote this fails for jmol/chimera view because the *file* is
+            // passed, not the structure data ID -
+            if (PDBfile.isCalcIdForFile(ala, findIdForPDBFile(pdbFile)))
+            {
+              parseSecStr = false;
+            }
+          }
+        }
+      }
+    }
+    return parseSecStr;
+  }
+
   public void addStructureMapping(StructureMapping sm)
   {
     mappings.add(sm);
@@ -624,13 +671,15 @@ public class StructureSelectionManager
    * @param maxChain
    * @param sqmpping
    * @param maxAlignseq
+   * @param siftsClient
+   *          client for retrieval of SIFTS mappings for this structure
    * @return
    * @throws SiftsException
    */
   private StructureMapping getStructureMapping(SequenceI seq,
           String pdbFile, String targetChainId, StructureFile pdb,
           PDBChain maxChain, jalview.datamodel.Mapping sqmpping,
-          AlignSeq maxAlignseq) throws SiftsException
+          AlignSeq maxAlignseq, SiftsClient siftsClient) throws SiftsException
   {
     StructureMapping curChainMapping = siftsClient
             .getSiftsStructureMapping(seq, pdbFile, targetChainId);
@@ -639,7 +688,7 @@ public class StructureSelectionManager
       PDBChain chain = pdb.findChain(targetChainId);
       if (chain != null)
       {
-        chain.transferResidueAnnotation(curChainMapping, sqmpping);
+        chain.transferResidueAnnotation(curChainMapping, null);
       }
     } catch (Exception e)
     {
diff --git a/src/jalview/util/HMMProbabilityDistributionAnalyser.java b/src/jalview/util/HMMProbabilityDistributionAnalyser.java
new file mode 100644
index 0000000..66ae552
--- /dev/null
+++ b/src/jalview/util/HMMProbabilityDistributionAnalyser.java
@@ -0,0 +1,978 @@
+package jalview.util;
+
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.HiddenMarkovModel;
+import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.FileParse;
+import jalview.io.HMMFile;
+import jalview.io.StockholmFile;
+import jalview.schemes.ResidueProperties;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.PrintWriter;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Random;
+import java.util.Scanner;
+import java.util.Vector;
+
+/**
+ * Processes probability data. The file indexes used in this program represent
+ * the index of the location of a family or hmm in their respective files,
+ * starting from 0.
+ * 
+ * @author TZVanaalten
+ *
+ */
+public class HMMProbabilityDistributionAnalyser
+{
+  AlignmentAnnotation reference = null;
+
+  Vector<SequenceI> sequences;
+
+  HiddenMarkovModel hmm;
+
+  // contains the raw data produced
+  List<ArrayList<Double>> raw = new ArrayList<>();
+
+  // contains binned data
+  Map<String, Double> binned = new HashMap<>();
+
+  // location of the family file
+  String families = "/media/sf_Shared_Folder/PFAM/Family/SeedFamilies.seed";
+
+  // location of the file containing the family-clan links
+  final static String FAMILIESTOCLAN = "/media/sf_Shared_Folder/PFAM/Family/Clanlinks.dat";
+
+  // location of the HMM file
+  String hmms = "/media/sf_Shared_Folder/PFAM/HMMs/Pfam-A.hmm";
+
+  // suffix for raw file
+  final static String RAW = "/Raw.csv";
+
+  // suffix for binned file
+  final static String BINNED = "/Binned.csv";
+
+  // normalisation scale
+  final static double SCALE = 1;
+
+  // current position in file
+  int currentFilePosition = 0;
+
+  final static String NL = "\n";
+
+  Random generator = new Random();
+
+  // current directory
+  String currentFolder;
+
+  boolean keepRaw = false;
+
+  /**
+   * Sets the working directory.
+   * 
+   * @param path
+   */
+  public void setFolder(String path)
+  {
+    currentFolder = path;
+  }
+
+  /**
+   * Moves a buffered reader forward in the file by a certain amount of entries.
+   * Each entry in the file is delimited by '//'.
+   * 
+   * @param index
+   *          The index of the location in the file.
+   * @param br
+   * @throws IOException
+   */
+  public void moveLocationBy(int index, BufferedReader br)
+          throws IOException
+  {
+    for (int i = 0; i < index; i++)
+    {
+      String line = br.readLine();
+      while (!"//".equals(line))
+      {
+        line = br.readLine();
+
+      }
+    }
+
+  }
+  
+  /**
+   * Analyses a specified number of families and then saves the data. Before
+   * analysing the data, the previous saved data will be imported and after
+   * analysing this, the data is exported back into the file. The file must be
+   * in flat file format.
+   * 
+   * @param increments
+   *          The number of families to read before saving.
+   * @throws IOException
+   */
+  public void run(int increments, boolean keepRawData) throws IOException
+  {
+    keepRaw = keepRawData;
+    try
+    {
+      readPreviousData(currentFolder);
+      BufferedReader posReader = new BufferedReader(
+              new FileReader(currentFolder + "/CurrentPosition.txt"));
+
+      String line = posReader.readLine();
+      posReader.close();
+      currentFilePosition = Integer.parseInt(line);
+    } catch (Exception e)
+    {
+      System.out.println("No previous data found");
+    }
+
+
+
+    BufferedReader inputSTO = new BufferedReader(new FileReader(families));
+    BufferedReader inputHMM = new BufferedReader(new FileReader(hmms));
+
+
+
+    moveLocationBy(currentFilePosition, inputHMM);
+    moveLocationBy(currentFilePosition, inputSTO);
+
+    int filesRead = 0;
+    int i = 0;
+    while (filesRead < increments)
+    {
+
+      readStockholm(inputSTO);
+
+      readHMM(inputHMM);
+
+        int count = countValidResidues();
+        processData(count);
+        filesRead++;
+
+      currentFilePosition++;
+      System.out.println(i);
+      i++;
+    }
+
+    PrintWriter p = new PrintWriter(
+            new File(currentFolder + "/CurrentPosition.txt"));
+    p.print(currentFilePosition);
+    p.close();
+    exportData(currentFolder);
+    raw.clear();
+    binned.clear();
+
+  }
+
+  /**
+   * Analyses all families and then saves the data. Before analysing the data,
+   * the previous saved data will be imported and after analysing this, the data
+   * is exported back into the file. The file must be in flat file format.
+   * 
+   * @param increments
+   *          The number of families to read before saving.
+   * @throws IOException
+   */
+  public void runToEnd(int minCount, int maxCount, boolean keepRawData,
+          boolean forClans)
+          throws IOException
+  {
+    keepRaw = keepRawData;
+    BufferedReader inputSTO = null;
+    BufferedReader inputHMM = null;
+    int size = 0;
+    int files = 1;
+    try
+    {
+    if (forClans)
+    {
+        files = 603;
+    }
+    int filesRead = 0;
+    for (int clan = 0; clan < files; clan++)
+    {
+      System.out.println(clan);
+      String clanPath = "";
+      int numberOfFamilies = 0;
+      if (forClans)
+      {
+        clanPath = currentFolder + "/Clan" + clan;
+          if (!new File(clanPath).exists())
+          {
+            continue;
+          }
+        BufferedReader famCountReader = new BufferedReader(
+                new FileReader(clanPath + "/NumberOfFamilies.txt"));
+        numberOfFamilies = Integer.parseInt(famCountReader.readLine());
+      }
+      else
+      {
+        numberOfFamilies = 1;
+      }
+      
+      for (int fam = 0; fam < numberOfFamilies; fam++)
+      {
+        if (forClans)
+        {
+          families = clanPath + "/Families/Fam" + fam + ".sto";
+          hmms = clanPath + "/HMMs/HMM" + fam + ".hmm";
+        }
+
+        inputSTO = new BufferedReader(new FileReader(families));
+        inputHMM = new BufferedReader(new FileReader(hmms));
+
+
+        int i = 0;
+        boolean endReached = atEnd(inputSTO);
+        while (!endReached)
+        {
+          readStockholm(inputSTO);
+          readHMM(inputHMM);
+
+        int count = countValidResidues();
+            if (count >= minCount && count < maxCount)
+            {
+              processData(count);
+            }
+        filesRead++;
+          System.out.println(filesRead);
+      endReached = atEnd(inputSTO);
+      }
+      }
+    }
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+    } finally
+    {
+      exportData(currentFolder);
+      raw.clear();
+      binned.clear();
+    }
+  }
+
+  /**
+   * Reads the previous data from both files
+   * 
+   * @param source
+   * @throws IOException
+   */
+  public void readPreviousData(String source) throws IOException
+  {
+    readBinned(source);
+    if (keepRaw)
+    {
+      readRaw(source);
+    }
+  }
+
+  /**
+   * Reads the previous data from the binned file.
+   * 
+   * @param source
+   * @throws IOException
+   */
+  public void readBinned(String source) throws IOException
+  {
+    BufferedReader input = new BufferedReader(
+            new FileReader(source + BINNED));
+    String line = input.readLine();
+    binned = new HashMap<>();
+    while (!("".equals(line) || line == null))
+    {
+      Scanner scanner = new Scanner(line);
+      scanner.useDelimiter(",");
+      String key = scanner.next();
+      String value = scanner.next();
+      binned.put(key, Double.valueOf(value));
+      scanner.close();
+      line = input.readLine();
+    }
+
+    input.close();
+  }
+
+  /**
+   * Reads the previous data from the raw file.
+   * 
+   * @param source
+   * @throws IOException
+   */
+  public void readRaw(String source) throws IOException
+  {
+    BufferedReader input = new BufferedReader(new FileReader(source + RAW));
+    String line = input.readLine();
+    if (line == null)
+    {
+      input.close();
+      return;
+    }
+    Scanner numberScanner = new Scanner(line);
+    numberScanner.useDelimiter(",");
+    raw = new ArrayList<>();
+    while (numberScanner.hasNext())
+    {
+      numberScanner.next();
+      raw.add(new ArrayList<Double>());
+    }
+    numberScanner.close();
+
+    line = input.readLine();
+    while (!("".equals(line) || line == null))
+    {
+      Scanner scanner = new Scanner(line);
+      scanner.useDelimiter(",");
+
+      int i = 0;
+      while (scanner.hasNext())
+      {
+        String value;
+        value = scanner.next();
+        if (!value.equals("EMPTY"))
+        {
+          raw.get(i).add(Double.parseDouble(value));
+        }
+        else
+        {
+          raw.get(i).add(null);
+        }
+
+        i++;
+      }
+      scanner.close();
+      line = input.readLine();
+    }
+
+    input.close();
+  }
+
+  /**
+   * Counts the number of valid residues in the sequence.
+   * 
+   * @return
+   */
+  public int countValidResidues()
+  {
+    int count = 0;
+
+    for (int width = 0; width < sequences.size(); width++)
+    {
+      for (int length = 1; length < hmm.getLength() + 1; length++)
+      {
+        char symbol;
+        int alignPos;
+        alignPos = hmm.getNodeMapPosition(length);
+
+        symbol = sequences.get(width).getCharAt(alignPos);
+        if (ResidueProperties.backgroundFrequencies.get("amino")
+                .containsKey(symbol))
+        {
+          count++;
+        }
+      }
+    }
+
+    return count;
+  }
+
+  /**
+   * Processes data, and stores it in both a raw and binned format.
+   * 
+   * @param count
+   */
+  public void processData(int count)
+  {
+    int rawPos = 0;
+    if (keepRaw)
+    {
+      raw.add(new ArrayList<Double>());
+      rawPos = raw.size() - 1;
+    }
+    Double total = 0d;
+    for (int width = 0; width < sequences.size(); width++)
+    {
+      for (int length = 1; length < hmm.getLength() + 1; length++)
+      {
+        char symbol;
+        int alignPos;
+        alignPos = hmm.getNodeMapPosition(length);
+        
+        symbol = sequences.get(width).getCharAt(alignPos);
+        if (ResidueProperties.backgroundFrequencies.get("amino")
+                .containsKey(symbol))
+        {
+          Double prob;
+          Float bfreq;
+          Double llr;
+          prob = hmm.getMatchEmissionProbability(alignPos, symbol);
+          bfreq = ResidueProperties.backgroundFrequencies.get("amino")
+                  .get(symbol);
+          if (prob == 0 || bfreq == 0)
+          {
+            System.out.println("error");
+          }
+          llr = Math.log(prob / bfreq);
+          if (keepRaw)
+          {
+            raw.get(rawPos).add(llr);
+          }
+
+          String output;
+          output = String.format("%.1f", llr);
+          total += Double.parseDouble(output);
+          if ("-0.0".equals(output))
+          {
+            output = "0.0";
+          }
+          if (binned.containsKey(output))
+          {
+            double prev = binned.get(output);
+            prev += (SCALE / count);
+            binned.put(output, prev);
+
+          }
+          else
+          {
+            binned.put(output, SCALE / count);
+          }
+        }
+      }
+    }
+    System.out.println(total / count);
+  }
+
+
+  /**
+   * Reads in the sequence data from a Stockholm file.
+   * 
+   * @param source
+   * @throws IOException
+   */
+  public void readStockholm(BufferedReader inputSTO) throws IOException
+  {
+    FileParse parserSTO = new FileParse(inputSTO, "", DataSourceType.FILE);
+    StockholmFile file = new StockholmFile(parserSTO);
+    Vector<AlignmentAnnotation> annots = file.getAnnotations();
+
+    for (AlignmentAnnotation annot : annots)
+    {
+      if (annot.label.contains("Reference"))
+      {
+        reference = annot;
+      }
+    }
+    sequences = file.getSeqs();
+  }
+
+  /**
+   * Reads in the HMM data from a HMMer file.
+   * 
+   * @param source
+   * @throws IOException
+   */
+  public void readHMM(BufferedReader inputHMM) throws IOException
+  {
+    FileParse parserHMM = new FileParse(inputHMM, "", DataSourceType.FILE);
+    HMMFile file = new HMMFile(parserHMM);
+    hmm = file.getHMM();
+
+
+  }
+
+  /**
+   * Exports both the binned and raw data into separate files.
+   * 
+   * @param location
+   * @throws FileNotFoundException
+   */
+  public void exportData(String location) throws FileNotFoundException
+  {
+    PrintWriter writerBin = new PrintWriter(new File(location + BINNED));
+    for (Map.Entry<String, Double> entry : binned.entrySet())
+    {
+      writerBin.println(entry.getKey() + "," + entry.getValue());
+    }
+    writerBin.close();
+    if (keepRaw)
+    {
+
+    PrintWriter writerRaw = new PrintWriter(new File(location + RAW));
+    
+    StringBuilder identifier = new StringBuilder();
+    
+    for (int i = 1; i < raw.size() + 1; i++)
+    {
+      identifier.append("Fam " + i + ",");
+    }
+    
+    writerRaw.println(identifier);
+    
+    boolean rowIsEmpty = false;
+    int row = 0;
+    while (!rowIsEmpty)
+    {
+      rowIsEmpty = true;
+      StringBuilder string = new StringBuilder();
+      for (int column = 0; column < raw.size(); column++)
+      {
+        if (raw.get(column).size() <= row)
+        {
+          string.append("EMPTY,");
+        }
+        else
+        {
+          string.append(raw.get(column).get(row) + ",");
+          rowIsEmpty = false;
+        }
+      }
+      row++;
+      writerRaw.println(string);
+    }
+    writerRaw.close();
+
+    }
+
+  }
+
+  /**
+   * Prints the specified family on the console.
+   * 
+   * @param index
+   * @throws IOException
+   */
+  public void printFam(int index) throws IOException
+  {
+    BufferedReader br = new BufferedReader(new FileReader(families));
+
+    moveLocationBy(index, br);
+
+    String line = br.readLine();
+
+    while (!"//".equals(line))
+    {
+      System.out.println(line);
+      line = br.readLine();
+    }
+    System.out.println(line);
+    br.close();
+
+  }
+
+  /**
+   * Prints the specified HMM on the console.
+   * 
+   * @param index
+   * @throws IOException
+   */
+  public void printHMM(int index) throws IOException
+  {
+    BufferedReader br = new BufferedReader(new FileReader(hmms));
+
+    moveLocationBy(index, br);
+
+    String line = br.readLine();
+
+    while (!"//".equals(line))
+    {
+      System.out.println(line);
+      line = br.readLine();
+    }
+    System.out.println(line);
+    br.close();
+
+  }
+
+  /**
+   * Prints the specified family to a .sto file.
+   * 
+   * @param index
+   * @throws IOException
+   */
+  public void exportFam(int index, String location) throws IOException
+  {
+    BufferedReader br = new BufferedReader(new FileReader(families));
+
+    moveLocationBy(index, br);
+
+    String line = br.readLine();
+    PrintWriter writer = new PrintWriter(
+            new FileOutputStream(new File(location), true));
+    while (!"//".equals(line))
+    {
+      writer.println(line);
+      line = br.readLine();
+    }
+    writer.println(line);
+    writer.close();
+    br.close();
+
+  }
+
+  public void exportFile(BufferedReader br, String location, boolean append)
+          throws IOException
+  {
+    String line = br.readLine();
+    PrintWriter writer = new PrintWriter(
+            new FileOutputStream(location, append));
+    while (!"//".equals(line))
+    {
+      writer.println(line);
+      line = br.readLine();
+    }
+    writer.println(line);
+    writer.close();
+
+
+  }
+
+  public String getHMMName(int index) throws IOException
+  {
+    String name;
+
+    BufferedReader nameFinder = new BufferedReader(new FileReader(hmms));
+
+    moveLocationBy(index, nameFinder);
+
+    nameFinder.readLine();
+
+    Scanner scanner = new Scanner(nameFinder.readLine());
+    name = scanner.next();
+    name = scanner.next();
+    scanner.close();
+    return name;
+  }
+
+  public String getFamilyName(int index) throws IOException
+  {
+    String name;
+
+    BufferedReader nameFinder = new BufferedReader(
+            new FileReader(families));
+
+    moveLocationBy(index, nameFinder);
+
+    nameFinder.readLine();
+
+    Scanner scanner = new Scanner(nameFinder.readLine());
+    name = scanner.next();
+    name = scanner.next();
+    name = scanner.next();
+    scanner.close();
+    return name;
+  }
+
+  /**
+   * Prints the specified family to a .hmm file.
+   * 
+   * @param index
+   * @throws IOException
+   */
+  public void exportHMM(int index, String location) throws IOException
+  {
+
+
+    BufferedReader br = new BufferedReader(new FileReader(hmms));
+
+    moveLocationBy(index, br);
+
+    String line = br.readLine();
+
+    PrintWriter writer = new PrintWriter(
+            new FileOutputStream(new File(location), true));
+    while (!"//".equals(line))
+    {
+      writer.println(line);
+      line = br.readLine();
+    }
+    writer.println(line);
+    writer.close();
+    br.close();
+
+  }
+  
+  /**
+   * Clears all raw, binned and current position data in the current directory.
+   * 
+   * @throws FileNotFoundException
+   */
+  public void clear() throws FileNotFoundException
+  {
+    PrintWriter pos = new PrintWriter(
+            currentFolder + "/CurrentPosition.txt");
+    pos.println("0");
+    
+    PrintWriter raw = new PrintWriter(currentFolder + RAW);
+    
+    PrintWriter bin = new PrintWriter(currentFolder + BINNED);
+    
+    pos.close();
+    bin.close();
+    raw.close();
+  }
+
+  public void sortIntoClans(String directory) throws IOException
+  {
+    BufferedReader clanFinder = new BufferedReader(new FileReader(FAMILIESTOCLAN));
+    BufferedReader familyReader = new BufferedReader(
+            new FileReader(families));
+    BufferedReader hmmReader = new BufferedReader(new FileReader(hmms));
+    int families = 0;
+    // moveLocationBy(7000, familyReader);
+    // moveLocationBy(7000, clanFinder);
+    // moveLocationBy(7000, hmmReader);
+    HashMap<String, Integer> clanIndexes = new HashMap<>();
+    ArrayList<Integer> familyCounts = new ArrayList<>();
+    int filePos = 0; 
+    int clanCount = 0;
+    String line;
+    line = clanFinder.readLine();
+    
+    while (!"".equals(line) && !" ".equals(line) && line != null)
+    {
+     String clanName;
+      boolean inClan = false;
+     while (!(line.indexOf("//") > -1))
+     {
+       
+      if (line.indexOf("#=GF CL") > -1)
+      {
+          families++;
+          System.out.println(families);
+          inClan = true;
+        Scanner scanner = new Scanner(line);
+        scanner.next();
+        scanner.next();
+        clanName = scanner.next();
+          scanner.close();
+        
+        if (!clanIndexes.containsKey(clanName))
+        {
+          clanIndexes.put(clanName, clanCount);
+            clanCount++;
+            familyCounts.add(0);
+        }
+
+
+          Integer clanI = clanIndexes.get(clanName);
+          String clanPath = directory + "/Clan" + clanI.toString();
+          createFolders(clanPath);
+
+          int index = clanIndexes.get(clanName);
+          exportFile(familyReader,
+                  clanPath + "/Families/Fam" + familyCounts.get(index)
+                          + ".sto",
+                  false);
+          exportFile(hmmReader,
+                  clanPath + "/HMMs/HMM" + familyCounts.get(index) + ".hmm",
+                  false);
+
+          int count = familyCounts.get(index);
+          count++;
+          familyCounts.set(index, count);
+      }
+        line = clanFinder.readLine();
+
+      }
+      if (!inClan)
+      {
+        moveLocationBy(1, familyReader);
+        moveLocationBy(1, hmmReader);
+      }
+      filePos++;
+      // System.out.println(filePos + " files read.");
+      line = clanFinder.readLine();
+
+     }
+    clanFinder.close();
+
+    for (int clan = 0; clan < clanCount; clan++)
+    {
+      PrintWriter writer = new PrintWriter(
+              directory + "/Clan" + clan + "/NumberOfFamilies.txt");
+      int count = familyCounts.get(clan);
+      writer.print(count);
+      writer.close();
+    }
+      
+    }
+
+  public String getFamilies()
+  {
+    return families;
+  }
+
+  public void setFamilies(String families)
+  {
+    this.families = currentFolder + families;
+  }
+
+  public String getHmms()
+  {
+    return hmms;
+  }
+
+  public void setHmms(String hmms)
+  {
+    this.hmms = currentFolder + hmms;
+  }
+    
+  public void alignWithinClan(String exportLocation, String clansLocation)
+          throws IOException, InterruptedException
+  {
+    int alignmentsExported = 0;
+    for (int clan = 0; clan < 604; clan++)
+    {
+      System.out.println(clan);
+      int famCount = 0;
+      String clanPath = clansLocation + "/Clan" + clan;
+      int numberOfFamilies;
+      BufferedReader br = new BufferedReader(
+              new FileReader(clanPath + "/NumberOfFamilies.txt"));
+      String line = br.readLine();
+      numberOfFamilies = Integer.parseInt(line);
+      br.close();
+      if (numberOfFamilies == 1)
+      {
+        continue;
+      }
+      final String commandExportLocation = exportLocation + "/Clan" + clan;
+      createFolders(commandExportLocation);
+      for (int family = 0; family < numberOfFamilies; family++)
+      {
+        famCount++;
+        ArrayList<Integer> indexes = new ArrayList<>();
+        for (int i = 0; i < numberOfFamilies; i++)
+        {
+          if (i != family)
+          {
+            indexes.add(i);
+          }
+        }
+
+        int hmmIndex = getRandom(indexes);
+        String famPath = clanPath + "/Families/Fam" + family + ".sto";
+        String hmmPath = clanPath + "/HMMs/HMM" + hmmIndex + ".hmm";
+        String command = "/media/sf_Shared_Folder/hmmer/binaries/hmmalign --mapali "
+                + clanPath + "/Families/Fam" + hmmIndex + ".sto"
+                + " --trim ";
+        command += hmmPath + " ";
+        command += famPath;
+        final int familyIndex = family;
+        final Process p = Runtime.getRuntime().exec(command);
+
+        new Thread(new Runnable()
+        {
+          @Override
+          public void run()
+          {
+            BufferedReader input = new BufferedReader(
+                    new InputStreamReader(p.getInputStream()));
+            String line = null;
+
+            try
+            {
+              PrintWriter writer = new PrintWriter(commandExportLocation
+                      + "/Families/Fam" + familyIndex + ".sto");
+              String lastLine = "";
+              boolean dataFound = false;
+              while ((line = input.readLine()) != null)
+              {
+                if (line.contains("#=GR") && !dataFound)
+                {
+                  writer.println(lastLine);
+                  dataFound = true;
+                }
+                if (line.contains("#") || dataFound || " ".equals(line)
+                        || "".equals(line) || "//".equals(line))
+                {
+                  writer.println(line);
+                }
+                lastLine = line;
+              }
+              writer.close();
+            } catch (IOException e)
+            {
+              e.printStackTrace();
+            }
+          }
+        }).start();
+
+        p.waitFor();
+
+        BufferedReader hmmExporter = new BufferedReader(
+                new FileReader(hmmPath));
+
+        exportFile(hmmExporter,
+                commandExportLocation + "/HMMs/HMM" + family + ".hmm",
+                false);
+
+        alignmentsExported++;
+
+
+      }
+      PrintWriter writer = new PrintWriter(
+              commandExportLocation + "/NumberOfFamilies.txt");
+      writer.print(famCount);
+      writer.close();
+    }
+
+  }
+
+  public boolean atEnd(BufferedReader br) throws IOException
+  {
+    boolean end = false;
+    br.mark(80);
+    String line = br.readLine();
+    if ("".equals(line) || line == null)
+    {
+      end = true;
+    }
+    br.reset();
+    return end;
+  }
+
+  public int getRandom(ArrayList<Integer> list)
+  {
+    if (!(list.size() > 0))
+    {
+      System.out.println("Error - size = " + list.size());
+    }
+    int index = generator.nextInt(list.size());
+    int value = list.get(index);
+    list.remove(index);
+    return value;
+  }
+
+  public void createFolders(String clanPath)
+  {
+    File clanFolder = new File(clanPath);
+    if (!clanFolder.exists())
+    {
+      clanFolder.mkdir();
+    }
+
+    File famFolder = new File(clanPath + "/Families");
+    File hmmFolder = new File(clanPath + "/HMMs");
+    if (!famFolder.exists())
+    {
+      famFolder.mkdir();
+      hmmFolder.mkdir();
+    }
+  }
+}
+
+
+
+
diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java
index c944345..81b9964 100644
--- a/src/jalview/util/MapList.java
+++ b/src/jalview/util/MapList.java
@@ -1021,70 +1021,15 @@ public class MapList
 
     for (int[] range : map.getFromRanges())
     {
-      addRange(range, fromShifts);
+      MappingUtils.addRange(range, fromShifts);
     }
     for (int[] range : map.getToRanges())
     {
-      addRange(range, toShifts);
+      MappingUtils.addRange(range, toShifts);
     }
   }
 
   /**
-   * Adds the given range to a list of ranges. If the new range just extends
-   * existing ranges, the current endpoint is updated instead.
-   * 
-   * @param range
-   * @param addTo
-   */
-  static void addRange(int[] range, List<int[]> addTo)
-  {
-    /*
-     * list is empty - add to it!
-     */
-    if (addTo.size() == 0)
-    {
-      addTo.add(range);
-      return;
-    }
-
-    int[] last = addTo.get(addTo.size() - 1);
-    boolean lastForward = last[1] >= last[0];
-    boolean newForward = range[1] >= range[0];
-
-    /*
-     * contiguous range in the same direction - just update endpoint
-     */
-    if (lastForward == newForward && last[1] == range[0])
-    {
-      last[1] = range[1];
-      return;
-    }
-
-    /*
-     * next range starts at +1 in forward sense - update endpoint
-     */
-    if (lastForward && newForward && range[0] == last[1] + 1)
-    {
-      last[1] = range[1];
-      return;
-    }
-
-    /*
-     * next range starts at -1 in reverse sense - update endpoint
-     */
-    if (!lastForward && !newForward && range[0] == last[1] - 1)
-    {
-      last[1] = range[1];
-      return;
-    }
-
-    /*
-     * just add the new range
-     */
-    addTo.add(range);
-  }
-
-  /**
    * Returns true if mapping is from forward strand, false if from reverse
    * strand. Result is just based on the first 'from' range that is not a single
    * position. Default is true unless proven to be false. Behaviour is not well
diff --git a/src/jalview/util/MappingUtils.java b/src/jalview/util/MappingUtils.java
index f5dd883..cd8821d 100644
--- a/src/jalview/util/MappingUtils.java
+++ b/src/jalview/util/MappingUtils.java
@@ -542,9 +542,11 @@ public final class MappingUtils
               toSequences, fromGapChar);
     }
 
-    for (int[] hidden : hiddencols.getHiddenColumnsCopy())
+    Iterator<int[]> regions = hiddencols.iterator();
+    while (regions.hasNext())
     {
-      mapHiddenColumns(hidden, codonFrames, newHidden, fromSequences,
+      mapHiddenColumns(regions.next(), codonFrames, newHidden,
+              fromSequences,
               toSequences, fromGapChar);
     }
     return; // mappedColumns;
@@ -1018,4 +1020,59 @@ public final class MappingUtils
       }
     }
   }
+
+  /**
+   * Adds the given range to a list of ranges. If the new range just extends
+   * existing ranges, the current endpoint is updated instead.
+   * 
+   * @param range
+   * @param addTo
+   */
+  public static void addRange(int[] range, List<int[]> addTo)
+  {
+    /*
+     * list is empty - add to it!
+     */
+    if (addTo.size() == 0)
+    {
+      addTo.add(range);
+      return;
+    }
+  
+    int[] last = addTo.get(addTo.size() - 1);
+    boolean lastForward = last[1] >= last[0];
+    boolean newForward = range[1] >= range[0];
+  
+    /*
+     * contiguous range in the same direction - just update endpoint
+     */
+    if (lastForward == newForward && last[1] == range[0])
+    {
+      last[1] = range[1];
+      return;
+    }
+  
+    /*
+     * next range starts at +1 in forward sense - update endpoint
+     */
+    if (lastForward && newForward && range[0] == last[1] + 1)
+    {
+      last[1] = range[1];
+      return;
+    }
+  
+    /*
+     * next range starts at -1 in reverse sense - update endpoint
+     */
+    if (!lastForward && !newForward && range[0] == last[1] - 1)
+    {
+      last[1] = range[1];
+      return;
+    }
+  
+    /*
+     * just add the new range
+     */
+    addTo.add(range);
+  }
 }
diff --git a/src/jalview/util/ProbabilityAnalyserKickstarter.java b/src/jalview/util/ProbabilityAnalyserKickstarter.java
new file mode 100644
index 0000000..59c0a9f
--- /dev/null
+++ b/src/jalview/util/ProbabilityAnalyserKickstarter.java
@@ -0,0 +1,221 @@
+package jalview.util;
+
+import java.io.IOException;
+import java.util.Scanner;
+
+/**
+ * This class contains the brain of the analyser program, and contains a number
+ * of commands for the processing of data.
+ * 
+ * @author TZVanaalten
+ *
+ */
+
+public class ProbabilityAnalyserKickstarter
+{
+
+  public static void main(String[] args)
+          throws IOException, InterruptedException
+  {
+
+    // this does all of the processing
+    HMMProbabilityDistributionAnalyser analyser = new HMMProbabilityDistributionAnalyser();
+
+    boolean running = true;
+    System.out.println("ACTIVATED");
+    while (running)
+    {
+      Scanner keyboard = new Scanner(System.in);
+      String command = keyboard.nextLine();
+
+      Scanner inputScanner = new Scanner(command);
+      // prints family to console. Syntax is printFam <index>
+      if (command.indexOf("printFam") > -1)
+      {
+        try
+        {
+          inputScanner.next();
+          int index = inputScanner.nextInt();
+          analyser.printFam(index);
+          continue;
+        } catch (Exception e)
+        {
+          System.out.println("Command failed");
+        }
+
+      }
+      // prints HMM to console. Syntax is printHMM <index>
+      if (command.indexOf("printHMM") > -1)
+      {
+        try
+        {
+        inputScanner.next();
+        int index = inputScanner.nextInt();
+        analyser.printHMM(index);
+        continue;
+        } catch (Exception e)
+        {
+          System.out.println("Command failed");
+        }
+      }
+      // prints family to file in current folder. Syntax is exportFam <index>.
+      if (command.indexOf("exportFam") > -1)
+      {
+        try
+        {
+        inputScanner.next();
+        int index = inputScanner.nextInt();
+          String location = inputScanner.next();
+          analyser.exportFam(index, location);
+        continue;
+        } catch (Exception e)
+        {
+          System.out.println("Command failed");
+        }
+      }
+      // prints HMM to file in current folder. Syntax is exportHMM <index>.
+      if (command.indexOf("exportHMM") > -1)
+      {
+        try
+        {
+        inputScanner.next();
+        int index = inputScanner.nextInt();
+          String location = inputScanner.next();
+          analyser.exportHMM(index, location);
+        continue;
+        } catch (Exception e)
+        {
+          System.out.println("Command failed");
+        }
+      }
+      // Processes data. Syntax is run <number of loops> <increments>. The
+      // number loops specifies the number of increments the program will run.
+      // After each increment, the data stored currently in the program is
+      // exported and re-read back into the program. This is to ensure that the
+      // program can be terminated without losing a large quantity of data. The
+      // increment is the number of families read per 'save'.
+      if (command.indexOf("run") > -1 && !(command.indexOf("ToEnd") > -1))
+      {
+        try
+        {
+
+        inputScanner.next();
+
+        int loops = inputScanner.nextInt();
+        int increments = inputScanner.nextInt();
+        boolean keepRaw = inputScanner.nextBoolean();
+
+        for (int i = 0; i < loops; i++)
+        {
+          analyser.run(increments, keepRaw);
+          System.out.println("Saved");
+        }
+        System.out.println("Task completed");
+        continue;
+        } catch (Exception e)
+        {
+          System.out.println("Command failed");
+        }
+        continue;
+      }
+      if ((command.indexOf("runToEnd") > -1))
+      {
+        try
+        {
+
+          inputScanner.next();
+          int minCount = inputScanner.nextInt();
+          int maxCount = inputScanner.nextInt();
+          boolean keepRaw = inputScanner.nextBoolean();
+          boolean forClans = inputScanner.nextBoolean();
+          analyser.runToEnd(minCount, maxCount, keepRaw, forClans);
+          System.out.println("Task completed");
+        } catch (Exception e)
+        {
+          System.out.println("Command failed");
+        }
+        continue;
+      }
+      // terminates program. Syntax is terminate.
+      if (command.indexOf("terminate") > -1)
+      {
+        running = false;
+        continue;
+      }
+      // clears files in current directory (Only a specific set of files).
+      // Syntax is clear.
+      if (command.indexOf("clear") > -1)
+      {
+        analyser.clear();
+        continue;
+      }
+      // changes current directory. Syntax is cd <directory>
+      if (command.indexOf("cd") > -1)
+      {
+        try
+        {
+        inputScanner.next();
+        analyser.setFolder(inputScanner.next());
+        } catch (Exception e)
+        {
+          System.out.println("Command failed");
+
+        }
+        continue;
+      }
+
+      if (command.indexOf("getFamName") > -1)
+      {
+        try
+        {
+        inputScanner.next();
+        System.out.println(analyser.getFamilyName(inputScanner.nextInt()));
+
+        } catch (Exception e)
+        {
+          System.out.println("Command failed");
+        }
+        continue;
+      }
+      if (command.indexOf("sortIntoClans") > -1)
+      {
+        inputScanner.next();
+        analyser.sortIntoClans(inputScanner.next());
+          continue;
+
+      }
+      if (command.indexOf("setFamilies") > -1)
+      {
+        inputScanner.next();
+        analyser.setFamilies(inputScanner.next());
+        continue;
+
+      }
+
+      if (command.indexOf("setHMMs") > -1)
+      {
+        inputScanner.next();
+        analyser.setHmms(inputScanner.next());
+        continue;
+
+      }
+
+      if (command.indexOf("alignWithinClans") > -1)
+      {
+        inputScanner.next();
+        String export = inputScanner.next();
+        String clans = inputScanner.next();
+        analyser.alignWithinClan(export, clans);
+        continue;
+
+      }
+
+      System.out.println("Unrecognised command");
+    }
+
+
+
+
+  }
+
+}
diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index a0cbff4..18c2aed 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -57,6 +57,7 @@ import jalview.viewmodel.styles.ViewStyle;
 import jalview.workers.AlignCalcManager;
 import jalview.workers.ComplementConsensusThread;
 import jalview.workers.ConsensusThread;
+import jalview.workers.InformationThread;
 import jalview.workers.StrucConsensusThread;
 
 import java.awt.Color;
@@ -67,6 +68,7 @@ import java.util.BitSet;
 import java.util.Deque;
 import java.util.HashMap;
 import java.util.Hashtable;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 
@@ -96,10 +98,69 @@ public abstract class AlignmentViewport
 
   protected Deque<CommandI> redoList = new ArrayDeque<>();
 
+  protected String sequenceSetID;
+
+  /*
+   * probably unused indicator that view is of a dataset rather than an
+   * alignment
+   */
+  protected boolean isDataset = false;
+
+  private Map<SequenceI, SequenceCollectionI> hiddenRepSequences;
+
+  protected ColumnSelection colSel = new ColumnSelection();
+
+  public boolean autoCalculateConsensus = true;
+
+  protected boolean autoCalculateStrucConsensus = true;
+
+  protected boolean ignoreGapsInConsensusCalculation = false;
+
+  protected boolean ignoreBelowBackGroundFrequencyCalculation = false;
+
+  protected boolean infoLetterHeight = false;
+
+  protected ResidueShaderI residueShading = new ResidueShader();
+
+  protected AlignmentAnnotation consensus;
+
+  protected AlignmentAnnotation complementConsensus;
+
+  protected AlignmentAnnotation occupancy;
+
+  protected AlignmentAnnotation strucConsensus;
+
+  protected AlignmentAnnotation conservation;
+
+  protected AlignmentAnnotation quality;
+
+  /**
+   * alignment displayed in the viewport
+   */
+  private AlignmentI alignment;
+
   /**
-   * alignment displayed in the viewport. Please use get/setter
+   * results of alignment consensus analysis for visible portion of view
+   */
+  protected ProfilesI consensusProfiles;
+
+  /**
+   * HMM profile for the alignment
+   */
+  protected ProfilesI hmmProfiles;
+
+  /**
+   * results of cDNA complement consensus visible portion of view
    */
-  protected AlignmentI alignment;
+  protected Hashtable[] hcomplementConsensus;
+
+  /**
+   * results of secondary structure base pair consensus for visible portion of
+   * view
+   */
+  protected Hashtable[] hStrucConsensus;
+
+  protected Conservation hconservation;
 
   public AlignmentViewport(AlignmentI al)
   {
@@ -580,14 +641,6 @@ public abstract class AlignmentViewport
     return alignment.getGapCharacter();
   }
 
-  protected String sequenceSetID;
-
-  /**
-   * probably unused indicator that view is of a dataset rather than an
-   * alignment
-   */
-  protected boolean isDataset = false;
-
   public void setDataset(boolean b)
   {
     isDataset = b;
@@ -598,18 +651,6 @@ public abstract class AlignmentViewport
     return isDataset;
   }
 
-  private Map<SequenceI, SequenceCollectionI> hiddenRepSequences;
-
-  protected ColumnSelection colSel = new ColumnSelection();
-
-  public boolean autoCalculateConsensus = true;
-
-  protected boolean autoCalculateStrucConsensus = true;
-
-  protected boolean ignoreGapsInConsensusCalculation = false;
-
-  protected ResidueShaderI residueShading = new ResidueShader();
-
   @Override
   public void setGlobalColourScheme(ColourSchemeI cs)
   {
@@ -682,41 +723,6 @@ public abstract class AlignmentViewport
   {
     return residueShading;
   }
-
-  protected AlignmentAnnotation consensus;
-
-  protected AlignmentAnnotation complementConsensus;
-
-  protected AlignmentAnnotation gapcounts;
-
-  protected AlignmentAnnotation strucConsensus;
-
-  protected AlignmentAnnotation conservation;
-
-  protected AlignmentAnnotation quality;
-
-  protected AlignmentAnnotation[] groupConsensus;
-
-  protected AlignmentAnnotation[] groupConservation;
-
-  /**
-   * results of alignment consensus analysis for visible portion of view
-   */
-  protected ProfilesI hconsensus = null;
-
-  /**
-   * results of cDNA complement consensus visible portion of view
-   */
-  protected Hashtable[] hcomplementConsensus = null;
-
-  /**
-   * results of secondary structure base pair consensus for visible portion of
-   * view
-   */
-  protected Hashtable[] hStrucConsensus = null;
-
-  protected Conservation hconservation = null;
-
   @Override
   public void setConservation(Conservation cons)
   {
@@ -736,9 +742,9 @@ public abstract class AlignmentViewport
   }
 
   @Override
-  public void setSequenceConsensusHash(ProfilesI hconsensus)
+  public void setConsensusProfiles(ProfilesI hconsensus)
   {
-    this.hconsensus = hconsensus;
+    this.consensusProfiles = hconsensus;
   }
 
   @Override
@@ -748,9 +754,21 @@ public abstract class AlignmentViewport
   }
 
   @Override
-  public ProfilesI getSequenceConsensusHash()
+  public ProfilesI getConsensusProfiles()
+  {
+    return consensusProfiles;
+  }
+
+  @Override
+  public void setHmmProfiles(ProfilesI info)
+  {
+    hmmProfiles = info;
+  }
+
+  @Override
+  public ProfilesI getHmmProfiles()
   {
-    return hconsensus;
+    return hmmProfiles;
   }
 
   @Override
@@ -791,9 +809,9 @@ public abstract class AlignmentViewport
   }
 
   @Override
-  public AlignmentAnnotation getAlignmentGapAnnotation()
+  public AlignmentAnnotation getOccupancyAnnotation()
   {
-    return gapcounts;
+    return occupancy;
   }
 
   @Override
@@ -882,6 +900,16 @@ public abstract class AlignmentViewport
     }
   }
 
+  @Override
+  public void initInformationWorker(final AlignmentViewPanel ap)
+  {
+    if (calculator
+            .getRegisteredWorkersOfClass(InformationThread.class) == null)
+    {
+      calculator.registerWorker(new InformationThread(this, ap));
+    }
+  }
+
   // --------START Structure Conservation
   public void updateStrucConsensus(final AlignmentViewPanel ap)
   {
@@ -945,12 +973,10 @@ public abstract class AlignmentViewport
     strucConsensus = null;
     conservation = null;
     quality = null;
-    groupConsensus = null;
-    groupConservation = null;
-    hconsensus = null;
+    consensusProfiles = null;
     hconservation = null;
     hcomplementConsensus = null;
-    gapcounts = null;
+    occupancy = null;
     calculator = null;
     residueShading = null; // may hold a reference to Consensus
     changeSupport = null;
@@ -1000,6 +1026,21 @@ public abstract class AlignmentViewport
   protected boolean showConsensusHistogram = true;
 
   /**
+   * should hmm profile be rendered by default
+   */
+  protected boolean hmmShowSequenceLogo = false;
+
+  /**
+   * should hmm profile be rendered normalised to row height
+   */
+  protected boolean hmmNormaliseSequenceLogo = false;
+
+  /**
+   * should information histograms be rendered by default
+   */
+  protected boolean hmmShowHistogram = true;
+
+  /**
    * @return the showConsensusProfile
    */
   @Override
@@ -1009,6 +1050,15 @@ public abstract class AlignmentViewport
   }
 
   /**
+   * @return the showInformationProfile
+   */
+  @Override
+  public boolean isShowHMMSequenceLogo()
+  {
+    return hmmShowSequenceLogo;
+  }
+
+  /**
    * @param showSequenceLogo
    *          the new value
    */
@@ -1026,6 +1076,18 @@ public abstract class AlignmentViewport
     this.showSequenceLogo = showSequenceLogo;
   }
 
+  public void setShowHMMSequenceLogo(boolean showHMMSequenceLogo)
+  {
+    if (showHMMSequenceLogo != this.hmmShowSequenceLogo)
+    {
+      this.hmmShowSequenceLogo = showHMMSequenceLogo;
+      // TODO: updateAnnotation if description (tooltip) will show
+      // profile in place of information content?
+      // calculator.updateAnnotationFor(InformationThread.class);
+    }
+    this.hmmShowSequenceLogo = showHMMSequenceLogo;
+  }
+
   /**
    * @param showConsensusHistogram
    *          the showConsensusHistogram to set
@@ -1036,6 +1098,14 @@ public abstract class AlignmentViewport
   }
 
   /**
+   * @param showInformationHistogram
+   */
+  public void setShowInformationHistogram(boolean showInformationHistogram)
+  {
+    this.hmmShowHistogram = showInformationHistogram;
+  }
+
+  /**
    * @return the showGroupConservation
    */
   public boolean isShowGroupConservation()
@@ -1081,6 +1151,17 @@ public abstract class AlignmentViewport
   }
 
   /**
+   * 
+   * @return flag to indicate if the information content histogram should be
+   *         rendered by default
+   */
+  @Override
+  public boolean isShowInformationHistogram()
+  {
+    return this.hmmShowHistogram;
+  }
+
+  /**
    * when set, updateAlignment will always ensure sequences are of equal length
    */
   private boolean padGaps = false;
@@ -1229,14 +1310,22 @@ public abstract class AlignmentViewport
     ignoreGapsInConsensusCalculation = b;
     if (ap != null)
     {
-      updateConsensus(ap);
       if (residueShading != null)
       {
         residueShading.setThreshold(residueShading.getThreshold(),
                 ignoreGapsInConsensusCalculation);
       }
     }
+  }
+
+  public void setIgnoreBelowBackground(boolean b, AlignmentViewPanel ap)
+  {
+    ignoreBelowBackGroundFrequencyCalculation = b;
+  }
 
+  public void setInfoLetterHeight(boolean b, AlignmentViewPanel ap)
+  {
+    infoLetterHeight = b;
   }
 
   private long sgrouphash = -1, colselhash = -1;
@@ -1293,6 +1382,18 @@ public abstract class AlignmentViewport
     return ignoreGapsInConsensusCalculation;
   }
 
+  @Override
+  public boolean isIgnoreBelowBackground()
+  {
+    return ignoreBelowBackGroundFrequencyCalculation;
+  }
+
+  @Override
+  public boolean isInfoLetterHeight()
+  {
+    return infoLetterHeight;
+  }
+
   // property change stuff
   // JBPNote Prolly only need this in the applet version.
   private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
@@ -1740,8 +1841,12 @@ public abstract class AlignmentViewport
     if (alignment.getHiddenColumns() != null
             && alignment.getHiddenColumns().hasHiddenColumns())
     {
-      selection = alignment.getHiddenColumns()
-              .getVisibleSequenceStrings(start, end, seqs);
+      for (i = 0; i < iSize; i++)
+      {
+        Iterator<int[]> blocks = alignment.getHiddenColumns()
+                .getVisContigsIterator(start, end + 1, false);
+        selection[i] = seqs[i].getSequenceStringFromIterator(blocks);
+      }
     }
     else
     {
@@ -1768,10 +1873,10 @@ public abstract class AlignmentViewport
       {
         if (start == 0)
         {
-          start = hidden.adjustForHiddenColumns(start);
+          start = hidden.visibleToAbsoluteColumn(start);
         }
 
-        end = hidden.getHiddenBoundaryRight(start);
+        end = hidden.getNextHiddenBoundary(false, start);
         if (start == end)
         {
           end = max;
@@ -1786,8 +1891,8 @@ public abstract class AlignmentViewport
 
       if (hidden != null && hidden.hasHiddenColumns())
       {
-        start = hidden.adjustForHiddenColumns(end);
-        start = hidden.getHiddenBoundaryLeft(start) + 1;
+        start = hidden.visibleToAbsoluteColumn(end);
+        start = hidden.getNextHiddenBoundary(true, start) + 1;
       }
     } while (end < max);
 
@@ -1809,13 +1914,13 @@ public abstract class AlignmentViewport
         AlignmentAnnotation clone = new AlignmentAnnotation(annot);
         if (selectedOnly && selectionGroup != null)
         {
-          alignment.getHiddenColumns().makeVisibleAnnotation(
+          clone.makeVisibleAnnotation(
                   selectionGroup.getStartRes(), selectionGroup.getEndRes(),
-                  clone);
+                  alignment.getHiddenColumns());
         }
         else
         {
-          alignment.getHiddenColumns().makeVisibleAnnotation(clone);
+          clone.makeVisibleAnnotation(alignment.getHiddenColumns());
         }
         ala.add(clone);
       }
@@ -1848,18 +1953,6 @@ public abstract class AlignmentViewport
     {
       alignment.padGaps();
     }
-    if (autoCalculateConsensus)
-    {
-      updateConsensus(ap);
-    }
-    if (hconsensus != null && autoCalculateConsensus)
-    {
-      updateConservation(ap);
-    }
-    if (autoCalculateStrucConsensus)
-    {
-      updateStrucConsensus(ap);
-    }
 
     // Reset endRes of groups if beyond alignment width
     int alWidth = alignment.getWidth();
@@ -1882,7 +1975,6 @@ public abstract class AlignmentViewport
 
     updateAllColourSchemes();
     calculator.restartWorkers();
-    // alignment.adjustSequenceAnnotations();
   }
 
   /**
@@ -1895,7 +1987,7 @@ public abstract class AlignmentViewport
     {
       rs.alignmentChanged(alignment, hiddenRepSequences);
 
-      rs.setConsensus(hconsensus);
+      rs.setConsensus(consensusProfiles);
       if (rs.conservationApplied())
       {
         rs.setConservation(Conservation.calculateConservation("All",
@@ -1920,7 +2012,7 @@ public abstract class AlignmentViewport
     // depending on if the user wants to see the annotation or not in a
     // specific alignment
 
-    if (hconsensus == null && !isDataset)
+    if (consensusProfiles == null && !isDataset)
     {
       if (!alignment.isNucleotide())
       {
@@ -1935,7 +2027,8 @@ public abstract class AlignmentViewport
               MessageManager.getString("label.consensus_descr"),
               new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
       initConsensus(consensus);
-      initGapCounts();
+
+      initOccupancy();
 
       initComplementConsensus();
     }
@@ -1994,20 +2087,20 @@ public abstract class AlignmentViewport
 
   // these should be extracted from the view model - style and settings for
   // derived annotation
-  private void initGapCounts()
+  private void initOccupancy()
   {
     if (showOccupancy)
     {
-      gapcounts = new AlignmentAnnotation("Occupancy",
+      occupancy = new AlignmentAnnotation("Occupancy",
               MessageManager.getString("label.occupancy_descr"),
               new Annotation[1], 0f, alignment.getHeight(),
               AlignmentAnnotation.BAR_GRAPH);
-      gapcounts.hasText = true;
-      gapcounts.autoCalculated = true;
-      gapcounts.scaleColLabel = true;
-      gapcounts.graph = AlignmentAnnotation.BAR_GRAPH;
+      occupancy.hasText = true;
+      occupancy.autoCalculated = true;
+      occupancy.scaleColLabel = true;
+      occupancy.graph = AlignmentAnnotation.BAR_GRAPH;
 
-      alignment.addAnnotation(gapcounts);
+      alignment.addAnnotation(occupancy);
     }
   }
 
@@ -2141,6 +2234,9 @@ public abstract class AlignmentViewport
     boolean showprf = isShowSequenceLogo();
     boolean showConsHist = isShowConsensusHistogram();
     boolean normLogo = isNormaliseSequenceLogo();
+    boolean showHMMPrf = isShowHMMSequenceLogo();
+    boolean showInfoHist = isShowInformationHistogram();
+    boolean normHMMLogo = isNormaliseHMMSequenceLogo();
 
     /**
      * TODO reorder the annotation rows according to group/sequence ordering on
@@ -2178,6 +2274,9 @@ public abstract class AlignmentViewport
           sg.setshowSequenceLogo(showprf);
           sg.setShowConsensusHistogram(showConsHist);
           sg.setNormaliseSequenceLogo(normLogo);
+          sg.setShowHMMSequenceLogo(showHMMPrf);
+          sg.setShowInformationHistogram(showInfoHist);
+          sg.setNormaliseHMMSequenceLogo(normHMMLogo);
         }
         if (conv)
         {
@@ -2781,7 +2880,7 @@ public abstract class AlignmentViewport
     int lastSeq = alignment.getHeight() - 1;
     List<AlignedCodonFrame> seqMappings = null;
     for (int seqNo = ranges
-            .getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
+            .getStartSeq(); seqNo <= lastSeq; seqNo++, seqOffset++)
     {
       sequence = getAlignment().getSequenceAt(seqNo);
       if (hiddenSequences != null && hiddenSequences.isHidden(sequence))
@@ -2938,6 +3037,19 @@ public abstract class AlignmentViewport
     return sq;
   }
 
+  public boolean hasReferenceAnnotation()
+  {
+    AlignmentAnnotation[] annots = this.alignment.getAlignmentAnnotation();
+    for (AlignmentAnnotation annot : annots)
+    {
+      if ("RF".equals(annot.label) || annot.label.contains("Reference"))
+      {
+        return true;
+      }
+    }
+    return false;
+  }
+
   @Override
   public void setCurrentTree(TreeModel tree)
   {
@@ -2949,4 +3061,26 @@ public abstract class AlignmentViewport
   {
     return currentTree;
   }
+
+  @Override
+  public boolean isNormaliseSequenceLogo()
+  {
+    return normaliseSequenceLogo;
+  }
+
+  public void setNormaliseSequenceLogo(boolean state)
+  {
+    normaliseSequenceLogo = state;
+  }
+
+  @Override
+  public boolean isNormaliseHMMSequenceLogo()
+  {
+    return hmmNormaliseSequenceLogo;
+  }
+
+  public void setNormaliseHMMSequenceLogo(boolean state)
+  {
+    hmmNormaliseSequenceLogo = state;
+  }
 }
diff --git a/src/jalview/viewmodel/OverviewDimensions.java b/src/jalview/viewmodel/OverviewDimensions.java
index 170f4e9..0235081 100644
--- a/src/jalview/viewmodel/OverviewDimensions.java
+++ b/src/jalview/viewmodel/OverviewDimensions.java
@@ -58,6 +58,10 @@ public abstract class OverviewDimensions
 
   protected int alheight;
 
+  protected float widthRatio;
+
+  protected float heightRatio;
+
   /**
    * Create an OverviewDimensions object
    * 
@@ -157,23 +161,25 @@ public abstract class OverviewDimensions
   public float getPixelsPerCol()
   {
     resetAlignmentDims();
-    return (float) width / alwidth;
+    return 1 / widthRatio;
   }
 
   public float getPixelsPerSeq()
   {
     resetAlignmentDims();
-    return (float) sequencesHeight / alheight;
+    return 1 / heightRatio;
   }
 
   public void setWidth(int w)
   {
     width = w;
+    widthRatio = (float) alwidth / width;
   }
 
   public void setHeight(int h)
   {
     sequencesHeight = h - graphHeight;
+    heightRatio = (float) alheight / sequencesHeight;
   }
 
   /**
@@ -273,14 +279,14 @@ public abstract class OverviewDimensions
 
     // boxX, boxY is the x,y location equivalent to startRes, startSeq
     int xPos = Math.min(startRes, alwidth - vpwidth + 1);
-    boxX = Math.round((float) xPos * width / alwidth);
-    boxY = Math.round((float) startSeq * sequencesHeight / alheight);
+    boxX = Math.round(xPos / widthRatio);
+    boxY = Math.round(startSeq / heightRatio);
 
     // boxWidth is the width in residues translated to pixels
-    boxWidth = Math.round((float) vpwidth * width / alwidth);
+    boxWidth = Math.round(vpwidth / widthRatio);
 
     // boxHeight is the height in sequences translated to pixels
-    boxHeight = Math.round((float) vpheight * sequencesHeight / alheight);
+    boxHeight = Math.round(vpheight / heightRatio);
   }
 
   /**
diff --git a/src/jalview/viewmodel/OverviewDimensionsHideHidden.java b/src/jalview/viewmodel/OverviewDimensionsHideHidden.java
index c158ce7..de90a21 100644
--- a/src/jalview/viewmodel/OverviewDimensionsHideHidden.java
+++ b/src/jalview/viewmodel/OverviewDimensionsHideHidden.java
@@ -50,6 +50,8 @@ public class OverviewDimensionsHideHidden extends OverviewDimensions
   public void updateViewportFromMouse(int mousex, int mousey,
           HiddenSequences hiddenSeqs, HiddenColumns hiddenCols)
   {
+    resetAlignmentDims();
+
     int xAsRes = getLeftXFromCentreX(mousex, hiddenCols);
     int yAsSeq = getTopYFromCentreY(mousey, hiddenSeqs);
 
@@ -61,24 +63,29 @@ public class OverviewDimensionsHideHidden extends OverviewDimensions
   public void adjustViewportFromMouse(int mousex, int mousey,
           HiddenSequences hiddenSeqs, HiddenColumns hiddenCols)
   {
+    resetAlignmentDims();
+
     // calculate translation in pixel terms:
     // get mouse location in viewport coords, add translation in viewport
     // coords, and update viewport as usual
-    int vpx = Math.round((float) mousex * alwidth / width);
-    int vpy = Math.round((float) mousey * alheight / sequencesHeight);
+    int vpx = Math.round(mousex * widthRatio);
+    int vpy = Math.round(mousey * heightRatio);
 
     updateViewportFromTopLeft(vpx + xdiff, vpy + ydiff, hiddenSeqs,
             hiddenCols);
 
   }
 
+  /**
+   * {@inheritDoc} Callers should have already called resetAlignmentDims to
+   * refresh alwidth, alheight and width/height ratios
+   */
   @Override
   protected void updateViewportFromTopLeft(int leftx, int topy,
           HiddenSequences hiddenSeqs, HiddenColumns hiddenCols)
   {
     int xAsRes = leftx;
     int yAsSeq = topy;
-    resetAlignmentDims();
 
     if (xAsRes < 0)
     {
@@ -147,7 +154,7 @@ public class OverviewDimensionsHideHidden extends OverviewDimensions
   public AlignmentColsCollectionI getColumns(AlignmentI al)
   {
     return new VisibleColsCollection(0,
-            ranges.getAbsoluteAlignmentWidth() - 1, al);
+            ranges.getAbsoluteAlignmentWidth() - 1, al.getHiddenColumns());
   }
 
   @Override
@@ -162,19 +169,30 @@ public class OverviewDimensionsHideHidden extends OverviewDimensions
   {
     alwidth = ranges.getVisibleAlignmentWidth();
     alheight = ranges.getVisibleAlignmentHeight();
+
+    widthRatio = (float) alwidth / width;
+    heightRatio = (float) alheight / sequencesHeight;
   }
 
+  /**
+   * {@inheritDoc} Callers should have already called resetAlignmentDims to
+   * refresh widthRatio
+   */
   @Override
   protected int getLeftXFromCentreX(int mousex, HiddenColumns hidden)
   {
-    int vpx = Math.round((float) mousex * alwidth / width);
+    int vpx = Math.round(mousex * widthRatio);
     return vpx - ranges.getViewportWidth() / 2;
   }
 
+  /**
+   * {@inheritDoc} Callers should have already called resetAlignmentDims to
+   * refresh heightRatio
+   */
   @Override
   protected int getTopYFromCentreY(int mousey, HiddenSequences hidden)
   {
-    int vpy = Math.round((float) mousey * alheight / sequencesHeight);
+    int vpy = Math.round(mousey * heightRatio);
     return vpy - ranges.getViewportHeight() / 2;
   }
 
@@ -182,10 +200,12 @@ public class OverviewDimensionsHideHidden extends OverviewDimensions
   public void setDragPoint(int x, int y, HiddenSequences hiddenSeqs,
           HiddenColumns hiddenCols)
   {
+    resetAlignmentDims();
+
     // get alignment position of x and box (can get directly from vpranges) and
     // calculate difference between the positions
-    int vpx = Math.round((float) x * alwidth / width);
-    int vpy = Math.round((float) y * alheight / sequencesHeight);
+    int vpx = Math.round(x * widthRatio);
+    int vpy = Math.round(y * heightRatio);
 
     xdiff = ranges.getStartRes() - vpx;
     ydiff = ranges.getStartSeq() - vpy;
diff --git a/src/jalview/viewmodel/OverviewDimensionsShowHidden.java b/src/jalview/viewmodel/OverviewDimensionsShowHidden.java
index 9dde16e..3aa6e1b 100644
--- a/src/jalview/viewmodel/OverviewDimensionsShowHidden.java
+++ b/src/jalview/viewmodel/OverviewDimensionsShowHidden.java
@@ -72,13 +72,15 @@ public class OverviewDimensionsShowHidden extends OverviewDimensions
   public void updateViewportFromMouse(int mousex, int mousey,
           HiddenSequences hiddenSeqs, HiddenColumns hiddenCols)
   {
+    resetAlignmentDims();
+
     // convert mousex and mousey to alignment units as well as
     // translating to top left corner of viewport - this is an absolute position
     int xAsRes = getLeftXFromCentreX(mousex, hiddenCols);
     int yAsSeq = getTopYFromCentreY(mousey, hiddenSeqs);
 
     // convert to visible positions
-    int visXAsRes = hiddenCols.findColumnPosition(xAsRes);
+    int visXAsRes = hiddenCols.absoluteToVisibleColumn(xAsRes);
     yAsSeq = hiddenSeqs.adjustForHiddenSeqs(
             hiddenSeqs.findIndexWithoutHiddenSeqs(yAsSeq));
     yAsSeq = Math.max(yAsSeq, 0); // -1 if before first visible sequence
@@ -93,27 +95,32 @@ public class OverviewDimensionsShowHidden extends OverviewDimensions
   public void adjustViewportFromMouse(int mousex, int mousey,
           HiddenSequences hiddenSeqs, HiddenColumns hiddenCols)
   {
+    resetAlignmentDims();
+
     // calculate translation in pixel terms:
     // get mouse location in viewport coords, add translation in viewport
     // coords,
     // convert back to pixel coords
     int vpx = Math.round((float) mousex * alwidth / width);
-    int visXAsRes = hiddenCols.findColumnPosition(vpx) + xdiff;
+    int visXAsRes = hiddenCols.absoluteToVisibleColumn(vpx) + xdiff;
 
-    int vpy = Math.round((float) mousey * alheight / sequencesHeight);
+    int vpy = Math.round(mousey * heightRatio);
     int visYAsRes = hiddenSeqs.findIndexWithoutHiddenSeqs(vpy) + ydiff;
 
     // update viewport accordingly
     updateViewportFromTopLeft(visXAsRes, visYAsRes, hiddenSeqs, hiddenCols);
   }
 
+  /**
+   * {@inheritDoc} Callers should have already called resetAlignmentDims to
+   * refresh alwidth, alheight and width/height ratios
+   */
   @Override
   protected void updateViewportFromTopLeft(int leftx, int topy,
           HiddenSequences hiddenSeqs, HiddenColumns hiddenCols)
   {
     int visXAsRes = leftx;
     int visYAsSeq = topy;
-    resetAlignmentDims();
 
     if (visXAsRes < 0)
     {
@@ -136,7 +143,7 @@ public class OverviewDimensionsShowHidden extends OverviewDimensions
     int vpwidth = ranges.getViewportWidth();
 
     // check in case we went off the edge of the alignment
-    int visAlignWidth = hiddenCols.findColumnPosition(alwidth - 1);
+    int visAlignWidth = hiddenCols.absoluteToVisibleColumn(alwidth - 1);
     if (visXAsRes + vpwidth - 1 > visAlignWidth)
     {
       // went past the end of the alignment, adjust backwards
@@ -144,8 +151,8 @@ public class OverviewDimensionsShowHidden extends OverviewDimensions
       // if last position was before the end of the alignment, need to update
       if (ranges.getEndRes() < visAlignWidth)
       {
-        visXAsRes = hiddenCols.findColumnPosition(hiddenCols
-                .subtractVisibleColumns(vpwidth - 1, alwidth - 1));
+        visXAsRes = hiddenCols.absoluteToVisibleColumn(hiddenCols
+                .offsetByVisibleColumns(-(vpwidth - 1), alwidth - 1));
       }
       else
       {
@@ -195,8 +202,8 @@ public class OverviewDimensionsShowHidden extends OverviewDimensions
           HiddenColumns hiddenCols)
   {
     // work with absolute values of startRes and endRes
-    int startRes = hiddenCols.adjustForHiddenColumns(ranges.getStartRes());
-    int endRes = hiddenCols.adjustForHiddenColumns(ranges.getEndRes());
+    int startRes = hiddenCols.visibleToAbsoluteColumn(ranges.getStartRes());
+    int endRes = hiddenCols.visibleToAbsoluteColumn(ranges.getEndRes());
 
     // work with absolute values of startSeq and endSeq
     int startSeq = hiddenSeqs.adjustForHiddenSeqs(ranges.getStartSeq());
@@ -225,20 +232,32 @@ public class OverviewDimensionsShowHidden extends OverviewDimensions
   {
     alwidth = ranges.getAbsoluteAlignmentWidth();
     alheight = ranges.getAbsoluteAlignmentHeight();
+
+    widthRatio = (float) alwidth / width;
+    heightRatio = (float) alheight / sequencesHeight;
   }
 
+
+  /**
+   * {@inheritDoc} Callers should have already called resetAlignmentDims to
+   * refresh widthRatio
+   */
   @Override
   protected int getLeftXFromCentreX(int mousex, HiddenColumns hidden)
   {
     int vpx = Math.round((float) mousex * alwidth / width);
-    return hidden.subtractVisibleColumns(ranges.getViewportWidth() / 2,
+    return hidden.offsetByVisibleColumns(-ranges.getViewportWidth() / 2,
             vpx);
   }
 
+  /**
+   * {@inheritDoc} Callers should have already called resetAlignmentDims to
+   * refresh heightRatio
+   */
   @Override
   protected int getTopYFromCentreY(int mousey, HiddenSequences hidden)
   {
-    int vpy = Math.round((float) mousey * alheight / sequencesHeight);
+    int vpy = Math.round(mousey * heightRatio);
     return hidden.subtractVisibleRows(ranges.getViewportHeight() / 2, vpy);
   }
 
@@ -246,12 +265,14 @@ public class OverviewDimensionsShowHidden extends OverviewDimensions
   public void setDragPoint(int x, int y, HiddenSequences hiddenSeqs,
           HiddenColumns hiddenCols)
   {
+    resetAlignmentDims();
+
     // get alignment position of x and box (can get directly from vpranges) and
     // calculate difference between the positions
-    int vpx = Math.round((float) x * alwidth / width);
-    int vpy = Math.round((float) y * alheight / sequencesHeight);
+    int vpx = Math.round(x * widthRatio);
+    int vpy = Math.round(y * heightRatio);
 
-    xdiff = ranges.getStartRes() - hiddenCols.findColumnPosition(vpx);
+    xdiff = ranges.getStartRes() - hiddenCols.absoluteToVisibleColumn(vpx);
     ydiff = ranges.getStartSeq()
             - hiddenSeqs.findIndexWithoutHiddenSeqs(vpy);
   }
diff --git a/src/jalview/viewmodel/ViewportRanges.java b/src/jalview/viewmodel/ViewportRanges.java
index c7a3fa1..691e492 100644
--- a/src/jalview/viewmodel/ViewportRanges.java
+++ b/src/jalview/viewmodel/ViewportRanges.java
@@ -609,14 +609,14 @@ public class ViewportRanges extends ViewportProperties
     }
     
     HiddenColumns hidden = al.getHiddenColumns();
-    while (x < hidden.adjustForHiddenColumns(startRes))
+    while (x < hidden.visibleToAbsoluteColumn(startRes))
     {
       if (!scrollRight(false))
       {
         break;
       }
     }
-    while (x > hidden.adjustForHiddenColumns(endRes))
+    while (x > hidden.visibleToAbsoluteColumn(endRes))
     {
       if (!scrollRight(true))
       {
@@ -638,7 +638,7 @@ public class ViewportRanges extends ViewportProperties
     boolean changedLocation = false;
 
     // convert the x,y location to visible coordinates
-    int visX = al.getHiddenColumns().findColumnPosition(x);
+    int visX = al.getHiddenColumns().absoluteToVisibleColumn(x);
     int visY = al.getHiddenSequences().findIndexWithoutHiddenSeqs(y);
 
     // if (vis_x,vis_y) is already visible don't do anything
diff --git a/src/jalview/workers/AlignCalcManager.java b/src/jalview/workers/AlignCalcManager.java
index 08ef3a2..6f0deab 100644
--- a/src/jalview/workers/AlignCalcManager.java
+++ b/src/jalview/workers/AlignCalcManager.java
@@ -74,7 +74,7 @@ public class AlignCalcManager implements AlignCalcManagerI
             .synchronizedList(new ArrayList<AlignCalcWorkerI>());
     updating = Collections.synchronizedMap(
             new Hashtable<Class<? extends AlignCalcWorkerI>, List<AlignCalcWorkerI>>());
-    canUpdate = new HashSet<AlignCalcWorkerI>();
+    canUpdate = new HashSet<>();
   }
 
   @Override
@@ -285,7 +285,7 @@ public class AlignCalcManager implements AlignCalcManagerI
   public List<AlignCalcWorkerI> getRegisteredWorkersOfClass(
           Class<? extends AlignCalcWorkerI> workerClass)
   {
-    List<AlignCalcWorkerI> workingClass = new ArrayList<AlignCalcWorkerI>();
+    List<AlignCalcWorkerI> workingClass = new ArrayList<>();
     synchronized (canUpdate)
     {
       for (AlignCalcWorkerI worker : canUpdate)
@@ -312,8 +312,8 @@ public class AlignCalcManager implements AlignCalcManagerI
   public void removeRegisteredWorkersOfClass(
           Class<? extends AlignCalcWorkerI> typeToRemove)
   {
-    List<AlignCalcWorkerI> removable = new ArrayList<AlignCalcWorkerI>();
-    Set<AlignCalcWorkerI> toremovannot = new HashSet<AlignCalcWorkerI>();
+    List<AlignCalcWorkerI> removable = new ArrayList<>();
+    Set<AlignCalcWorkerI> toremovannot = new HashSet<>();
     synchronized (restartable)
     {
       for (AlignCalcWorkerI worker : restartable)
@@ -363,7 +363,7 @@ public class AlignCalcManager implements AlignCalcManagerI
      * first just find those to remove (to avoid
      * ConcurrentModificationException)
      */
-    List<AlignCalcWorkerI> toRemove = new ArrayList<AlignCalcWorkerI>();
+    List<AlignCalcWorkerI> toRemove = new ArrayList<>();
     for (AlignCalcWorkerI worker : restartable)
     {
       if (worker.involves(ann))
diff --git a/src/jalview/workers/ConsensusThread.java b/src/jalview/workers/ConsensusThread.java
index 335529c..d6a4488 100644
--- a/src/jalview/workers/ConsensusThread.java
+++ b/src/jalview/workers/ConsensusThread.java
@@ -50,7 +50,7 @@ public class ConsensusThread extends AlignCalcWorker
     try
     {
       AlignmentAnnotation consensus = getConsensusAnnotation();
-      AlignmentAnnotation gap = getGapAnnotation();
+      AlignmentAnnotation gap = getOccupancyAnnotation();
       if ((consensus == null && gap == null) || calcMan.isPending(this))
       {
         calcMan.workerComplete(this);
@@ -119,7 +119,7 @@ public class ConsensusThread extends AlignCalcWorker
   {
     AlignmentAnnotation consensus = getConsensusAnnotation();
     consensus.annotations = new Annotation[aWidth];
-    AlignmentAnnotation gap = getGapAnnotation();
+    AlignmentAnnotation gap = getOccupancyAnnotation();
     if (gap != null)
     {
       gap.annotations = new Annotation[aWidth];
@@ -137,7 +137,7 @@ public class ConsensusThread extends AlignCalcWorker
     ProfilesI hconsensus = AAFrequency.calculate(aseqs, width, 0, width,
             true);
 
-    alignViewport.setSequenceConsensusHash(hconsensus);
+    alignViewport.setConsensusProfiles(hconsensus);
     setColourSchemeConsensus(hconsensus);
   }
 
@@ -176,9 +176,9 @@ public class ConsensusThread extends AlignCalcWorker
    * 
    * @return
    */
-  protected AlignmentAnnotation getGapAnnotation()
+  protected AlignmentAnnotation getOccupancyAnnotation()
   {
-    return alignViewport.getAlignmentGapAnnotation();
+    return alignViewport.getOccupancyAnnotation();
   }
 
   /**
@@ -199,10 +199,10 @@ public class ConsensusThread extends AlignCalcWorker
             && hconsensus != null)
     {
       deriveConsensus(consensus, hconsensus);
-      AlignmentAnnotation gap = getGapAnnotation();
-      if (gap != null)
+      AlignmentAnnotation occupancy = getOccupancyAnnotation();
+      if (occupancy != null)
       {
-        deriveGap(gap, hconsensus);
+        deriveOccupancy(occupancy, hconsensus);
       }
     }
   }
@@ -219,7 +219,6 @@ public class ConsensusThread extends AlignCalcWorker
   protected void deriveConsensus(AlignmentAnnotation consensusAnnotation,
           ProfilesI hconsensus)
   {
-
     long nseq = getSequences().length;
     AAFrequency.completeConsensus(consensusAnnotation, hconsensus,
             hconsensus.getStartColumn(), hconsensus.getEndColumn() + 1,
@@ -235,11 +234,11 @@ public class ConsensusThread extends AlignCalcWorker
    * @param hconsensus
    *          the computed consensus data
    */
-  protected void deriveGap(AlignmentAnnotation gapAnnotation,
+  protected void deriveOccupancy(AlignmentAnnotation gapAnnotation,
           ProfilesI hconsensus)
   {
     long nseq = getSequences().length;
-    AAFrequency.completeGapAnnot(gapAnnotation, hconsensus,
+    AAFrequency.completeOccupancyAnnot(gapAnnotation, hconsensus,
             hconsensus.getStartColumn(), hconsensus.getEndColumn() + 1,
             nseq);
   }
@@ -252,6 +251,6 @@ public class ConsensusThread extends AlignCalcWorker
   protected Object getViewportConsensus()
   {
     // TODO convert ComplementConsensusThread to use Profile
-    return alignViewport.getSequenceConsensusHash();
+    return alignViewport.getConsensusProfiles();
   }
 }
diff --git a/src/jalview/workers/InformationThread.java b/src/jalview/workers/InformationThread.java
new file mode 100644
index 0000000..d42598c
--- /dev/null
+++ b/src/jalview/workers/InformationThread.java
@@ -0,0 +1,311 @@
+package jalview.workers;
+
+import jalview.analysis.AAFrequency;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenMarkovModel;
+import jalview.datamodel.ProfilesI;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
+
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * This class calculates HMM Information Content annotations, based on any HMM
+ * consensus sequences and their HMM models. HMM consensus sequences may be
+ * present for the whole alignment, or subgroups of it.
+ *
+ */
+public class InformationThread extends AlignCalcWorker
+{
+  public static final String HMM_CALC_ID = "HMM";
+
+  /**
+   * Constructor
+   * 
+   * @param alignViewport
+   * @param alignPanel
+   */
+  public InformationThread(AlignViewportI alignViewport,
+          AlignmentViewPanel alignPanel)
+  {
+    super(alignViewport, alignPanel);
+  }
+
+  /**
+   * Recomputes Information annotations for any HMM consensus sequences (for
+   * alignment and/or groups)
+   */
+  @Override
+  public void run()
+  {
+    if (calcMan.isPending(this))
+    {
+      return;
+    }
+    calcMan.notifyStart(this);
+    // long started = System.currentTimeMillis();
+
+    try
+    {
+      if (calcMan.isPending(this))
+      {
+        // another instance of this is waiting to run
+        calcMan.workerComplete(this);
+        return;
+      }
+      while (!calcMan.notifyWorking(this))
+      {
+        // another thread in progress, wait my turn
+        try
+        {
+          if (ap != null)
+          {
+            ap.paintAlignment(false, false);
+          }
+          Thread.sleep(200);
+        } catch (Exception ex)
+        {
+          ex.printStackTrace();
+        }
+      }
+      if (alignViewport.isClosed())
+      {
+        abortAndDestroy();
+        return;
+      }
+
+      AlignmentI alignment = alignViewport.getAlignment();
+      int aWidth = alignment == null ? -1 : alignment.getWidth();
+      if (aWidth < 0)
+      {
+        calcMan.workerComplete(this);
+        return;
+      }
+
+      /*
+       * compute information profiles for any HMM consensus sequences
+       * for the alignment or sub-groups
+       */
+      computeProfiles(alignment);
+
+      /*
+       * construct the corresponding annotations
+       */
+      updateAnnotation();
+
+      if (ap != null)
+      {
+        ap.adjustAnnotationHeight();
+        ap.paintAlignment(true, true);
+      }
+    } catch (OutOfMemoryError error)
+    {
+      calcMan.disableWorker(this);
+      ap.raiseOOMWarning("calculating information", error);
+    } finally
+    {
+      calcMan.workerComplete(this);
+    }
+  }
+
+  /**
+   * Computes HMM profiles for any HMM consensus sequences (for alignment or
+   * subgroups). Any alignment profile computed is stored on the viewport, any
+   * group profile computed is stored on the respective sequence group.
+   * 
+   * @param alignment
+   * @see AlignViewportI#setHmmProfiles(ProfilesI)
+   */
+  protected void computeProfiles(AlignmentI alignment)
+  {
+    int width = alignment.getWidth();
+
+    /*
+     * alignment HMM profile
+     */
+    SequenceI seq = alignment.getHmmConsensus();
+    if (seq != null)
+    {
+      HiddenMarkovModel hmm = seq.getHMM();
+      ProfilesI hmmProfiles = AAFrequency.calculateHMMProfiles(hmm, width,
+              0, width, alignViewport.isIgnoreBelowBackground(),
+              alignViewport.isInfoLetterHeight());
+      alignViewport.setHmmProfiles(hmmProfiles);
+    }
+
+    /*
+     * group HMM profiles
+     */
+    List<SequenceGroup> groups = alignment.getGroups();
+    for (SequenceGroup group : groups)
+    {
+      seq = group.getHmmConsensus();
+      if (seq != null)
+      {
+        HiddenMarkovModel hmm = seq.getHMM();
+        ProfilesI hmmProfiles = AAFrequency.calculateHMMProfiles(hmm, width,
+                0, width, group.isIgnoreBelowBackground(),
+                group.isUseInfoLetterHeight());
+        group.setHmmProfiles(hmmProfiles);
+      }
+    }
+  }
+
+  /**
+   * gets the sequences on the alignment on the viewport.
+   * 
+   * @return
+   */
+  protected SequenceI[] getSequences()
+  {
+    return alignViewport.getAlignment().getSequencesArray();
+  }
+
+  /**
+   * Get the Gap annotation for the alignment
+   * 
+   * @return
+   */
+  protected AlignmentAnnotation getGapAnnotation()
+  {
+    return alignViewport.getOccupancyAnnotation();
+  }
+
+  /**
+   * Computes Information Content annotation for any HMM consensus sequences
+   * (for alignment or groups), and updates (or adds) the annotation to the
+   * sequence and the alignment
+   */
+  @Override
+  public void updateAnnotation()
+  {
+    AlignmentI alignment = alignViewport.getAlignment();
+
+    float maxInformation = 0f;
+    List<AlignmentAnnotation> infos = new ArrayList<>();
+
+    /*
+     * annotation for alignment HMM consensus if present
+     */
+    SequenceI hmmSeq = alignment.getHmmConsensus();
+    ProfilesI profile = alignViewport.getHmmProfiles();
+    float m = updateInformationAnnotation(hmmSeq, profile, null, infos);
+    maxInformation = Math.max(maxInformation, m);
+
+    /*
+     * annotation for group HMM consensus if present
+     */
+    for (SequenceGroup group : alignment.getGroups())
+    {
+      hmmSeq = group.getHmmConsensus();
+      ProfilesI profiles = group.getHmmProfiles();
+      m = updateInformationAnnotation(hmmSeq, profiles, group, infos);
+      maxInformation = Math.max(maxInformation, m);
+    }
+
+    /*
+     * maxInformation holds the maximum value of information score;
+     * set this as graphMax in all annotations to scale them all the same
+     */
+    for (AlignmentAnnotation ann : infos)
+    {
+      ann.graphMax = maxInformation;
+    }
+  }
+
+  /**
+   * Updates (and first constructs if necessary) an HMM Profile information
+   * content annotation for a sequence. The <code>group</code> argument is null
+   * for the whole alignment annotation, not null for a subgroup annotation. The
+   * updated annotation is added to the <code>infos</code> list. Answers the
+   * maximum information content value of any annotation (for use as a scaling
+   * factor for display).
+   * 
+   * @param seq
+   * @param profile
+   * @param group
+   * @param infos
+   * @return
+   */
+  protected float updateInformationAnnotation(SequenceI seq,
+          ProfilesI profile, SequenceGroup group,
+          List<AlignmentAnnotation> infos)
+  {
+    if (seq == null || profile == null)
+    {
+      return 0f;
+    }
+
+    AlignmentAnnotation ann = findOrCreateAnnotation(seq, group);
+
+    seq.addAlignmentAnnotation(ann);
+    infos.add(ann);
+
+    float max = AAFrequency.completeInformation(ann, profile,
+            profile.getStartColumn(), profile.getEndColumn() + 1);
+
+    return max;
+  }
+
+  /**
+   * A helper method that first searches for the HMM annotation that matches the
+   * group reference (null for the whole alignment annotation). If found, its
+   * sequence reference is updated to the given sequence (the recomputed HMM
+   * consensus sequence). If not found, it is created. This supports both
+   * creating the annotation the first time hmmbuild is run, and updating it if
+   * hmmbuild is re-run.
+   * 
+   * @param seq
+   * @param group
+   * @return
+   */
+  AlignmentAnnotation findOrCreateAnnotation(SequenceI seq,
+          SequenceGroup group)
+  {
+    /*
+     * can't use Alignment.findOrCreateAnnotation here because we 
+     * want to update, rather than match on, the sequence ref
+     */
+    AlignmentAnnotation info = null;
+
+    AlignmentI alignment = alignViewport.getAlignment();
+    AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
+    if (anns != null)
+    {
+      for (AlignmentAnnotation ann : anns)
+      {
+        if (HMM_CALC_ID.equals(ann.getCalcId()) && group == ann.groupRef)
+        {
+          info = ann;
+          info.setSequenceRef(seq);
+          info.label = seq.getName(); // in case group name changed!
+          break;
+        }
+      }
+    }
+
+    if (info == null)
+    {
+      int aWidth = alignment.getWidth();
+      String desc = MessageManager
+              .getString("label.information_description");
+      float graphMax = 6.52f; // todo where does this value derive from?
+      info = new AlignmentAnnotation(seq.getName(), desc,
+              new Annotation[aWidth], 0f, graphMax,
+              AlignmentAnnotation.BAR_GRAPH);
+      info.setCalcId(HMM_CALC_ID);
+      info.setSequenceRef(seq);
+      info.groupRef = group;
+      info.hasText = true;
+      alignment.addAnnotation(info);
+    }
+
+    return info;
+  }
+}
diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index fb8864d..1677eca 100644
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -61,6 +61,8 @@ public class DBRefFetcher implements Runnable
 {
   private static final String NEWLINE = System.lineSeparator();
 
+  public static final String TRIM_RETRIEVED_SEQUENCES = "TRIM_FETCHED_DATASET_SEQS";
+
   public interface FetchFinishedListenerI
   {
     void finished();
@@ -139,7 +141,7 @@ public class DBRefFetcher implements Runnable
             .getSequenceFetcherSingleton(progressIndicatorFrame);
     // set default behaviour for transferring excess sequence data to the
     // dataset
-    trimDsSeqs = Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true);
+    trimDsSeqs = Cache.getDefault(TRIM_RETRIEVED_SEQUENCES, true);
     if (sources == null)
     {
       setDatabaseSources(featureSettings, isNucleotide);
diff --git a/src/jalview/ws/dbsources/Pfam.java b/src/jalview/ws/dbsources/Pfam.java
index 0227e35..8877c34 100644
--- a/src/jalview/ws/dbsources/Pfam.java
+++ b/src/jalview/ws/dbsources/Pfam.java
@@ -20,6 +20,7 @@
  */
 package jalview.ws.dbsources;
 
+import jalview.bin.Cache;
 import jalview.datamodel.DBRefSource;
 
 import com.stevesoft.pat.Regex;
@@ -34,6 +35,9 @@ import com.stevesoft.pat.Regex;
  */
 abstract public class Pfam extends Xfam
 {
+  static final String PFAM_BASEURL_KEY = "PFAM_BASEURL";
+
+  private static final String DEFAULT_PFAM_BASEURL = "https://pfam.xfam.org";
 
   public Pfam()
   {
@@ -48,7 +52,6 @@ abstract public class Pfam extends Xfam
   @Override
   public String getAccessionSeparator()
   {
-    // TODO Auto-generated method stub
     return null;
   }
 
@@ -60,7 +63,6 @@ abstract public class Pfam extends Xfam
   @Override
   public Regex getAccessionValidator()
   {
-    // TODO Auto-generated method stub
     return null;
   }
 
@@ -91,17 +93,14 @@ abstract public class Pfam extends Xfam
   @Override
   public String getDbVersion()
   {
-    // TODO Auto-generated method stub
     return null;
   }
 
-  /**
-   * Returns base URL for selected Pfam alignment type
-   * 
-   * @return PFAM URL stub for this DbSource
-   */
   @Override
-  protected abstract String getXFAMURL();
+  protected String getURLPrefix()
+  {
+    return Cache.getDefault(PFAM_BASEURL_KEY, DEFAULT_PFAM_BASEURL);
+  }
 
   /*
    * (non-Javadoc)
diff --git a/src/jalview/ws/dbsources/PfamFull.java b/src/jalview/ws/dbsources/PfamFull.java
index ec9fcbb..0600427 100644
--- a/src/jalview/ws/dbsources/PfamFull.java
+++ b/src/jalview/ws/dbsources/PfamFull.java
@@ -31,20 +31,8 @@ public class PfamFull extends Pfam
     super();
   }
 
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.ws.dbsources.Pfam#getPFAMURL()
-   */
-  @Override
-  protected String getXFAMURL()
-  {
-    return "http://pfam.xfam.org/family/";
-
-  }
-
   @Override
-  public String getXFAMURLSUFFIX()
+  public String getURLSuffix()
   {
     return "/alignment/full";
   }
diff --git a/src/jalview/ws/dbsources/PfamSeed.java b/src/jalview/ws/dbsources/PfamSeed.java
index 33c39b1..dff8a17 100644
--- a/src/jalview/ws/dbsources/PfamSeed.java
+++ b/src/jalview/ws/dbsources/PfamSeed.java
@@ -33,19 +33,8 @@ public class PfamSeed extends Pfam
     super();
   }
 
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.ws.dbsources.Pfam#getPFAMURL()
-   */
-  @Override
-  protected String getXFAMURL()
-  {
-    return "http://pfam.xfam.org/family/";
-  }
-
   @Override
-  public String getXFAMURLSUFFIX()
+  public String getURLSuffix()
   {
     return "/alignment/seed";
   }
diff --git a/src/jalview/ws/dbsources/Rfam.java b/src/jalview/ws/dbsources/Rfam.java
index 97f73d0..1d9d99a 100644
--- a/src/jalview/ws/dbsources/Rfam.java
+++ b/src/jalview/ws/dbsources/Rfam.java
@@ -20,6 +20,7 @@
  */
 package jalview.ws.dbsources;
 
+import jalview.bin.Cache;
 import jalview.datamodel.DBRefSource;
 
 import com.stevesoft.pat.Regex;
@@ -31,6 +32,15 @@ import com.stevesoft.pat.Regex;
  */
 abstract public class Rfam extends Xfam
 {
+  static final String RFAM_BASEURL_KEY = "RFAM_BASEURL";
+
+  private static final String DEFAULT_RFAM_BASEURL = "https://rfam.xfam.org";
+
+  @Override
+  protected String getURLPrefix()
+  {
+    return Cache.getDefault(RFAM_BASEURL_KEY, DEFAULT_RFAM_BASEURL);
+  }
 
   public Rfam()
   {
@@ -46,7 +56,6 @@ abstract public class Rfam extends Xfam
   @Override
   public String getAccessionSeparator()
   {
-    // TODO Auto-generated method stub
     return null;
   }
 
@@ -58,7 +67,6 @@ abstract public class Rfam extends Xfam
   @Override
   public Regex getAccessionValidator()
   {
-    // TODO Auto-generated method stub
     return null;
   }
 
@@ -82,18 +90,9 @@ abstract public class Rfam extends Xfam
   @Override
   public String getDbVersion()
   {
-    // TODO Auto-generated method stub
     return null;
   }
 
-  /**
-   * Returns base URL for selected Rfam alignment type
-   * 
-   * @return RFAM URL stub for this DbSource
-   */
-  @Override
-  protected abstract String getXFAMURL();
-
   /*
    * (non-Javadoc)
    * 
diff --git a/src/jalview/ws/dbsources/RfamFull.java b/src/jalview/ws/dbsources/RfamFull.java
index b2ca31a..d815336 100644
--- a/src/jalview/ws/dbsources/RfamFull.java
+++ b/src/jalview/ws/dbsources/RfamFull.java
@@ -33,20 +33,8 @@ public class RfamFull extends Rfam
     super();
   }
 
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.ws.dbsources.Rfam#getXFAMURL()
-   */
-  @Override
-  protected String getXFAMURL()
-  {
-    return "http://rfam.xfam.org/family/";
-
-  }
-
   @Override
-  public String getXFAMURLSUFFIX()
+  public String getURLSuffix()
   {
     return "/alignment/full";
   }
diff --git a/src/jalview/ws/dbsources/RfamSeed.java b/src/jalview/ws/dbsources/RfamSeed.java
index f714547..a74e829 100644
--- a/src/jalview/ws/dbsources/RfamSeed.java
+++ b/src/jalview/ws/dbsources/RfamSeed.java
@@ -33,19 +33,8 @@ public class RfamSeed extends Rfam
     super();
   }
 
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.ws.dbsources.Rfam#getRFAMURL()
-   */
-  @Override
-  protected String getXFAMURL()
-  {
-    return "http://rfam.xfam.org/family/";
-  }
-
   @Override
-  public String getXFAMURLSUFFIX()
+  public String getURLSuffix()
   {
     // to download gzipped file add '?gzip=1'
     return "/alignment/stockholm";
diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index 73775cf..6b09eb6 100644
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -20,6 +20,7 @@
  */
 package jalview.ws.dbsources;
 
+import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
@@ -52,6 +53,8 @@ import com.stevesoft.pat.Regex;
  */
 public class Uniprot extends DbSourceProxyImpl
 {
+  private static final String DEFAULT_UNIPROT_DOMAIN = "https://www.uniprot.org";
+
   private static final String BAR_DELIMITER = "|";
 
   /*
@@ -67,6 +70,11 @@ public class Uniprot extends DbSourceProxyImpl
     super();
   }
 
+  private String getDomain()
+  {
+    return Cache.getDefault("UNIPROT_DOMAIN", DEFAULT_UNIPROT_DOMAIN);
+  }
+
   /*
    * (non-Javadoc)
    * 
@@ -163,7 +171,7 @@ public class Uniprot extends DbSourceProxyImpl
               "(UNIPROT\\|?|UNIPROT_|UNIREF\\d+_|UNIREF\\d+\\|?)", "");
       AlignmentI al = null;
 
-      String downloadstring = "http://www.uniprot.org/uniprot/" + queries
+      String downloadstring = getDomain() + "/uniprot/" + queries
               + ".xml";
       URL url = null;
       URLConnection urlconn = null;
diff --git a/src/jalview/ws/dbsources/Xfam.java b/src/jalview/ws/dbsources/Xfam.java
index 26291eb..b83f558 100644
--- a/src/jalview/ws/dbsources/Xfam.java
+++ b/src/jalview/ws/dbsources/Xfam.java
@@ -42,7 +42,12 @@ public abstract class Xfam extends DbSourceProxyImpl
     super();
   }
 
-  protected abstract String getXFAMURL();
+  /**
+   * the base URL for this Xfam-like service
+   * 
+   * @return
+   */
+  protected abstract String getURLPrefix();
 
   @Override
   public abstract String getDbVersion();
@@ -57,8 +62,7 @@ public abstract class Xfam extends DbSourceProxyImpl
     // retrieved.
     startQuery();
     // TODO: trap HTTP 404 exceptions and return null
-    String xfamUrl = getXFAMURL() + queries.trim().toUpperCase()
-            + getXFAMURLSUFFIX();
+    String xfamUrl = getURL(queries);
 
     if (Cache.log != null)
     {
@@ -83,6 +87,12 @@ public abstract class Xfam extends DbSourceProxyImpl
     return rcds;
   }
 
+  String getURL(String queries)
+  {
+    return getURLPrefix() + "/family/" + queries.trim().toUpperCase()
+            + getURLSuffix();
+  }
+
   /**
    * Pfam and Rfam provide alignments
    */
@@ -97,7 +107,7 @@ public abstract class Xfam extends DbSourceProxyImpl
    * 
    * @return "" for most Xfam sources
    */
-  public String getXFAMURLSUFFIX()
+  public String getURLSuffix()
   {
     return "";
   }
diff --git a/src/jalview/ws/jws1/JPredThread.java b/src/jalview/ws/jws1/JPredThread.java
index a239625..23d9eb0 100644
--- a/src/jalview/ws/jws1/JPredThread.java
+++ b/src/jalview/ws/jws1/JPredThread.java
@@ -235,8 +235,7 @@ class JPredThread extends JWS1Thread implements WSClientI
           {
             // Adjust input view for gaps
             // propagate insertions into profile
-            alhidden = HiddenColumns.propagateInsertions(profileseq, al,
-                    input);
+            alhidden = al.propagateInsertions(profileseq, input);
           }
         }
       }
diff --git a/src/jalview/ws/jws2/MsaWSThread.java b/src/jalview/ws/jws2/MsaWSThread.java
index db6e03f..c4fc66b 100644
--- a/src/jalview/ws/jws2/MsaWSThread.java
+++ b/src/jalview/ws/jws2/MsaWSThread.java
@@ -75,7 +75,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
     /**
      * input
      */
-    ArrayList<compbio.data.sequence.FastaSequence> seqs = new ArrayList<compbio.data.sequence.FastaSequence>();
+    ArrayList<compbio.data.sequence.FastaSequence> seqs = new ArrayList<>();
 
     /**
      * output
@@ -139,7 +139,6 @@ class MsaWSThread extends AWS2Thread implements WSClientI
       compbio.data.sequence.FastaSequence seq;
       for (int i = 0, n = 0; i < seqs.length; i++)
       {
-
         String newname = jalview.analysis.SeqsetUtils.unique_name(i); // same
         // for
         // any
@@ -379,7 +378,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
 
     public List<Argument> getJabaArguments()
     {
-      List<Argument> newargs = new ArrayList<Argument>();
+      List<Argument> newargs = new ArrayList<>();
       if (preset != null && preset instanceof JabaWsParamSet)
       {
         newargs.addAll(((JabaWsParamSet) preset).getjabaArguments());
@@ -931,7 +930,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
   void displayResults(boolean newFrame)
   {
     // view input or result data for each block
-    List<AlignmentOrder> alorders = new ArrayList<AlignmentOrder>();
+    List<AlignmentOrder> alorders = new ArrayList<>();
     SequenceI[][] results = new SequenceI[jobs.length][];
     AlignmentOrder[] orders = new AlignmentOrder[jobs.length];
     String lastProgram = null;
@@ -981,7 +980,6 @@ class MsaWSThread extends AWS2Thread implements WSClientI
     if (newFrame)
     {
       displayInNewFrame(al, alorders, hidden);
-
     }
     else
     {
@@ -1077,7 +1075,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
     else
     {
       // construct a non-redundant ordering set
-      List<String> names = new ArrayList<String>();
+      List<String> names = new ArrayList<>();
       for (int i = 0, l = alorders.size(); i < l; i++)
       {
         String orderName = " Region " + i;
diff --git a/src/jalview/ws/params/ValueConstrainI.java b/src/jalview/ws/params/ValueConstrainI.java
index da46745..47f454a 100644
--- a/src/jalview/ws/params/ValueConstrainI.java
+++ b/src/jalview/ws/params/ValueConstrainI.java
@@ -29,7 +29,7 @@ public interface ValueConstrainI
 
   public enum ValueType
   {
-    Integer, Float, String
+    Integer, Float, String, Double
   };
 
   ValueType getType();
diff --git a/src/jalview/ws/params/simple/DoubleParameter.java b/src/jalview/ws/params/simple/DoubleParameter.java
new file mode 100644
index 0000000..d6ccf46
--- /dev/null
+++ b/src/jalview/ws/params/simple/DoubleParameter.java
@@ -0,0 +1,89 @@
+package jalview.ws.params.simple;
+
+import jalview.ws.params.ParameterI;
+import jalview.ws.params.ValueConstrainI;
+
+/**
+ * 
+ * @author TZVanaalten
+ *
+ */
+public class DoubleParameter extends Option implements ParameterI
+{
+  Double defval;
+
+  Double min, max;
+
+  @Override
+  public ValueConstrainI getValidValue()
+  {
+    return new ValueConstrainI()
+    {
+
+      @Override
+      public ValueType getType()
+      {
+        return ValueType.Double;
+      }
+
+      @Override
+      public Number getMin()
+      {
+        if (min < max)
+        {
+          return min;
+        }
+        else
+        {
+          return null;
+        }
+      }
+
+      @Override
+      public Number getMax()
+      {
+        if (min < max)
+        {
+          return max;
+        }
+        else
+        {
+          return null;
+        }
+      }
+    };
+  }
+
+  public DoubleParameter(DoubleParameter parm)
+  {
+    super(parm);
+    max = parm.max;
+    min = parm.min;
+  }
+
+  public DoubleParameter(String name, String description, boolean required,
+          Double defValue, Double min, Double max)
+  {
+    super(name, description, required, String.valueOf(defValue), null, null,
+            null);
+    defval = defValue;
+    this.min = min;
+    this.max = max;
+  }
+
+  public DoubleParameter(String name, String description, boolean required,
+          Double defValue, Double value, Double min, Double max)
+  {
+    super(name, description, required, String.valueOf(defValue),
+            String.valueOf(value), null, null);
+    defval = defValue;
+    this.min = min;
+    this.max = max;
+  }
+
+  @Override
+  public DoubleParameter copy()
+  {
+    return new DoubleParameter(this);
+  }
+}
diff --git a/src/jalview/ws/params/simple/LogarithmicParameter.java b/src/jalview/ws/params/simple/LogarithmicParameter.java
new file mode 100644
index 0000000..91ed03a
--- /dev/null
+++ b/src/jalview/ws/params/simple/LogarithmicParameter.java
@@ -0,0 +1,101 @@
+package jalview.ws.params.simple;
+
+import jalview.ws.params.ParameterI;
+import jalview.ws.params.ValueConstrainI;
+
+/**
+ * 
+ * @author TZVanaalten
+ *
+ */
+public class LogarithmicParameter extends Option implements ParameterI
+{
+  Double defval;
+
+  Double min, max;
+
+  Double base;
+
+  @Override
+  public ValueConstrainI getValidValue()
+  {
+    return new ValueConstrainI()
+    {
+
+      @Override
+      public ValueType getType()
+      {
+        return ValueType.Double;
+      }
+
+      @Override
+      public Number getMin()
+      {
+        if (min < max)
+        {
+          return min;
+        }
+        else
+        {
+          return null;
+        }
+      }
+
+      @Override
+      public Number getMax()
+      {
+        if (min < max)
+        {
+          return max;
+        }
+        else
+        {
+          return null;
+        }
+      }
+    };
+  }
+
+  public LogarithmicParameter(LogarithmicParameter parm)
+  {
+    super(parm);
+    max = parm.max;
+    min = parm.min;
+    base = parm.base;
+  }
+
+  public LogarithmicParameter(String name, String description,
+          boolean required, Double defValue, Double min, Double max,
+          Double base)
+  {
+    super(name, description, required, String.valueOf(defValue), null, null,
+            null);
+    defval = defValue;
+    this.min = min * 1000000;
+    this.max = max * 1000000;
+    this.base = base;
+  }
+
+  public LogarithmicParameter(String name, String description,
+          boolean required, Double defValue, Double value, Double min,
+          Double max, Double base)
+  {
+    super(name, description, required, String.valueOf(defValue),
+            String.valueOf(value), null, null);
+    defval = defValue;
+    this.min = min * 1000000;
+    this.max = max * 1000000;
+    this.base = base;
+  }
+
+  @Override
+  public LogarithmicParameter copy()
+  {
+    return new LogarithmicParameter(this);
+  }
+
+  public Double getBase()
+  {
+    return base;
+  }
+}
diff --git a/src/jalview/ws/params/simple/StringParameter.java b/src/jalview/ws/params/simple/StringParameter.java
new file mode 100644
index 0000000..1d6a37e
--- /dev/null
+++ b/src/jalview/ws/params/simple/StringParameter.java
@@ -0,0 +1,118 @@
+package jalview.ws.params.simple;
+
+import jalview.ws.params.ParameterI;
+import jalview.ws.params.ValueConstrainI;
+
+import java.net.URL;
+import java.util.List;
+
+public class StringParameter extends Option implements ParameterI
+{
+
+  @Override
+  public URL getFurtherDetails()
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public boolean isRequired()
+  {
+    // TODO Auto-generated method stub
+    return false;
+  }
+
+  @Override
+  public String getDescription()
+  {
+    // TODO Auto-generated method stub
+    return description;
+  }
+
+  @Override
+  public List<String> getPossibleValues()
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public String getName()
+  {
+    // TODO Auto-generated method stub
+    return name;
+  }
+
+  @Override
+  public String getValue()
+  {
+    // TODO Auto-generated method stub
+    return value;
+  }
+
+  @Override
+  public void setValue(String selectedItem)
+  {
+    value = selectedItem;
+
+  }
+
+  @Override
+  public ValueConstrainI getValidValue()
+  {
+    // TODO Auto-generated method stub
+    return new StringValueConstrain();
+  }
+
+  @Override
+  public ParameterI copy()
+  {
+    return new StringParameter(this);
+  }
+
+  private class StringValueConstrain implements ValueConstrainI
+  {
+
+    @Override
+    public ValueType getType()
+    {
+      return ValueType.String;
+    }
+
+    @Override
+    public Number getMax()
+    {
+      return null;
+    }
+
+    @Override
+    public Number getMin()
+    {
+      return null;
+    }
+
+  }
+
+  public StringParameter(StringParameter parm)
+  {
+    this.name = parm.name;
+    this.defvalue = parm.defvalue;
+  }
+
+  public StringParameter(String name, String description, boolean required,
+          String defValue)
+  {
+    super(name, description, required, String.valueOf(defValue), null, null,
+            null);
+    this.defvalue = defValue;
+  }
+
+  public StringParameter(String name, String description, boolean required,
+          String defValue, String value)
+  {
+    super(name, description, required, String.valueOf(defValue),
+            String.valueOf(value), null, null);
+    this.defvalue = defValue;
+  }
+}
diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index 68af7c3..b5f9653 100644
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -92,14 +92,24 @@ public class SiftsClient implements SiftsClientI
 
   private CoordinateSys seqCoordSys = CoordinateSys.UNIPROT;
 
+  /**
+   * PDB sequence position to sequence coordinate mapping as derived from SIFTS
+   * record for the identified SeqCoordSys Used for lift-over from sequence
+   * derived from PDB (with first extracted PDBRESNUM as 'start' to the sequence
+   * being annotated with PDB data
+   */
+  private jalview.datamodel.Mapping seqFromPdbMapping;
+
   private static final int BUFFER_SIZE = 4096;
 
-  public static final int UNASSIGNED = -1;
+  public static final int UNASSIGNED = Integer.MIN_VALUE;
 
   private static final int PDB_RES_POS = 0;
 
   private static final int PDB_ATOM_POS = 1;
 
+  private static final int PDBE_POS = 2;
+
   private static final String NOT_OBSERVED = "Not_Observed";
 
   private static final String SIFTS_FTP_BASE_URL = "http://ftp.ebi.ac.uk/pub/databases/msd/sifts/xml/";
@@ -413,6 +423,11 @@ public class SiftsClient implements SiftsClientI
   public StructureMapping getSiftsStructureMapping(SequenceI seq,
           String pdbFile, String chain) throws SiftsException
   {
+    SequenceI aseq = seq;
+    while (seq.getDatasetSequence() != null)
+    {
+      seq = seq.getDatasetSequence();
+    }
     structId = (chain == null) ? pdbId : pdbId + "|" + chain;
     System.out.println("Getting SIFTS mapping for " + structId + ": seq "
             + seq.getName());
@@ -435,8 +450,9 @@ public class SiftsClient implements SiftsClientI
     HashMap<Integer, int[]> mapping = getGreedyMapping(chain, seq, ps);
 
     String mappingOutput = mappingDetails.toString();
-    StructureMapping siftsMapping = new StructureMapping(seq, pdbFile,
-            pdbId, chain, mapping, mappingOutput);
+    StructureMapping siftsMapping = new StructureMapping(aseq, pdbFile,
+            pdbId, chain, mapping, mappingOutput, seqFromPdbMapping);
+
     return siftsMapping;
   }
 
@@ -444,8 +460,8 @@ public class SiftsClient implements SiftsClientI
   public HashMap<Integer, int[]> getGreedyMapping(String entityId,
           SequenceI seq, java.io.PrintStream os) throws SiftsException
   {
-    List<Integer> omitNonObserved = new ArrayList<Integer>();
-    int nonObservedShiftIndex = 0;
+    List<Integer> omitNonObserved = new ArrayList<>();
+    int nonObservedShiftIndex = 0,pdbeNonObserved=0;
     // System.out.println("Generating mappings for : " + entityId);
     Entity entity = null;
     entity = getEntityById(entityId);
@@ -476,7 +492,7 @@ public class SiftsClient implements SiftsClientI
     TreeMap<Integer, String> resNumMap = new TreeMap<Integer, String>();
     List<Segment> segments = entity.getSegment();
     SegmentHelperPojo shp = new SegmentHelperPojo(seq, mapping, resNumMap,
-            omitNonObserved, nonObservedShiftIndex);
+            omitNonObserved, nonObservedShiftIndex,pdbeNonObserved);
     processSegments(segments, shp);
     try
     {
@@ -498,15 +514,61 @@ public class SiftsClient implements SiftsClientI
     {
       throw new SiftsException("SIFTS mapping failed");
     }
+    // also construct a mapping object between the seq-coord sys and the PDB seq's coord sys
 
     Integer[] keys = mapping.keySet().toArray(new Integer[0]);
     Arrays.sort(keys);
     seqStart = keys[0];
     seqEnd = keys[keys.length - 1];
-
+    List<int[]> from=new ArrayList<>(),to=new ArrayList<>();
+    int[]_cfrom=null,_cto=null;
     String matchedSeq = originalSeq;
-    if (seqStart != UNASSIGNED)
+    if (seqStart != UNASSIGNED) // fixme! seqStart can map to -1 for a pdb sequence that starts <-1
     {
+      for (int seqps:keys)
+      {
+        int pdbpos = mapping.get(seqps)[PDBE_POS];
+        if (pdbpos == UNASSIGNED)
+        {
+          // not correct - pdbpos might be -1, but leave it for now
+          continue;
+        }
+        if (_cfrom==null || seqps!=_cfrom[1]+1)
+        {
+          _cfrom = new int[] { seqps,seqps};
+          from.add(_cfrom);
+          _cto = null; // discontinuity
+        } else {
+          _cfrom[1]= seqps;
+        }
+        if (_cto==null || pdbpos!=1+_cto[1])
+        {
+          _cto = new int[] { pdbpos,pdbpos};
+          to.add(_cto);
+        } else {
+          _cto[1] = pdbpos;
+        }
+      }
+      _cfrom = new int[from.size() * 2];
+      _cto = new int[to.size() * 2];
+      int p = 0;
+      for (int[] range : from)
+      {
+        _cfrom[p++] = range[0];
+        _cfrom[p++] = range[1];
+      }
+      ;
+      p = 0;
+      for (int[] range : to)
+      {
+        _cto[p++] = range[0];
+        _cto[p++] = range[1];
+      }
+      ;
+
+      seqFromPdbMapping = new jalview.datamodel.Mapping(null, _cto, _cfrom,
+              1,
+              1);
       pdbStart = mapping.get(seqStart)[PDB_RES_POS];
       pdbEnd = mapping.get(seqEnd)[PDB_RES_POS];
       int orignalSeqStart = seq.getStart();
@@ -559,6 +621,8 @@ public class SiftsClient implements SiftsClientI
     TreeMap<Integer, String> resNumMap = shp.getResNumMap();
     List<Integer> omitNonObserved = shp.getOmitNonObserved();
     int nonObservedShiftIndex = shp.getNonObservedShiftIndex();
+    int pdbeNonObservedCount = shp.getPdbeNonObserved();
+    int firstPDBResNum = UNASSIGNED;
     for (Segment segment : segments)
     {
       // System.out.println("Mapping segments : " + segment.getSegId() + "\\"s
@@ -566,6 +630,9 @@ public class SiftsClient implements SiftsClientI
       List<Residue> residues = segment.getListResidue().getResidue();
       for (Residue residue : residues)
       {
+        boolean isObserved = isResidueObserved(residue);
+        int pdbeIndex = getLeadingIntegerValue(residue.getDbResNum(),
+                UNASSIGNED);
         int currSeqIndex = UNASSIGNED;
         List<CrossRefDb> cRefDbs = residue.getCrossRefDb();
         CrossRefDb pdbRefDb = null;
@@ -574,6 +641,19 @@ public class SiftsClient implements SiftsClientI
           if (cRefDb.getDbSource().equalsIgnoreCase(DBRefSource.PDB))
           {
             pdbRefDb = cRefDb;
+            if (firstPDBResNum == UNASSIGNED)
+            {
+              firstPDBResNum = getLeadingIntegerValue(cRefDb.getDbResNum(),
+                      UNASSIGNED);
+            }
+            else
+            {
+              if (isObserved)
+              {
+                // after we find the first observed residue we just increment
+                firstPDBResNum++;
+              }
+            }
           }
           if (cRefDb.getDbCoordSys().equalsIgnoreCase(seqCoordSys.getName())
                   && isAccessionMatched(cRefDb.getDbAccessionId()))
@@ -586,11 +666,45 @@ public class SiftsClient implements SiftsClientI
             }
           }
         }
+        if (!isObserved)
+        {
+          ++pdbeNonObservedCount;
+        }
+        if (seqCoordSys == seqCoordSys.PDB) // FIXME: is seqCoordSys ever PDBe
+                                            // ???
+        {
+          // if the sequence has a primary reference to the PDB, then we are
+          // dealing with a sequence extracted directly from the PDB. In that
+          // case, numbering is PDBe - non-observed residues
+          currSeqIndex = seq.getStart() - 1 + pdbeIndex;
+        }
+        if (!isObserved)
+        {
+          if (seqCoordSys != CoordinateSys.UNIPROT) // FIXME: PDB or PDBe only
+                                                    // here
+          {
+            // mapping to PDB or PDBe so we need to bookkeep for the
+            // non-observed
+            // SEQRES positions
+            omitNonObserved.add(currSeqIndex);
+            ++nonObservedShiftIndex;
+          }
+        }
         if (currSeqIndex == UNASSIGNED)
         {
+          // change in logic - unobserved residues with no currSeqIndex
+          // corresponding are still counted in both nonObservedShiftIndex and
+          // pdbeIndex...
           continue;
         }
-        if (currSeqIndex >= seq.getStart() && currSeqIndex <= seq.getEnd())
+        // if (currSeqIndex >= seq.getStart() && currSeqIndex <= seqlength) //
+        // true
+                                                                         // numbering
+                                                                         // is
+                                                                         // not
+                                                                         // up
+                                                                         // to
+                                                                         // seq.getEnd()
         {
 
           int resNum = (pdbRefDb == null)
@@ -599,22 +713,18 @@ public class SiftsClient implements SiftsClientI
                   : getLeadingIntegerValue(pdbRefDb.getDbResNum(),
                           UNASSIGNED);
 
-          if (isResidueObserved(residue)
-                  || seqCoordSys == CoordinateSys.UNIPROT)
+          if (isObserved)
           {
             char resCharCode = ResidueProperties
                     .getSingleCharacterCode(ResidueProperties
                             .getCanonicalAminoAcid(residue.getDbResName()));
             resNumMap.put(currSeqIndex, String.valueOf(resCharCode));
+
+            int[] mappingcols = new int[] { Integer.valueOf(resNum),
+                UNASSIGNED, isObserved ? firstPDBResNum : UNASSIGNED };
+
+            mapping.put(currSeqIndex - nonObservedShiftIndex, mappingcols);
           }
-          else
-          {
-            omitNonObserved.add(currSeqIndex);
-            ++nonObservedShiftIndex;
-          }
-          mapping.put(currSeqIndex - nonObservedShiftIndex,
-                  new int[]
-                  { Integer.valueOf(resNum), UNASSIGNED });
         }
       }
     }
@@ -904,17 +1014,36 @@ public class SiftsClient implements SiftsClientI
 
     private int nonObservedShiftIndex;
 
+    /**
+     * count of number of 'not observed' positions in the PDB record's SEQRES
+     * (total number of residues with coordinates == length(SEQRES) -
+     * pdbeNonObserved
+     */
+    private int pdbeNonObserved;
+
     public SegmentHelperPojo(SequenceI seq, HashMap<Integer, int[]> mapping,
             TreeMap<Integer, String> resNumMap,
-            List<Integer> omitNonObserved, int nonObservedShiftIndex)
+            List<Integer> omitNonObserved, int nonObservedShiftIndex,
+            int pdbeNonObserved)
     {
       setSeq(seq);
       setMapping(mapping);
       setResNumMap(resNumMap);
       setOmitNonObserved(omitNonObserved);
       setNonObservedShiftIndex(nonObservedShiftIndex);
+      setPdbeNonObserved(pdbeNonObserved);
+
     }
 
+    public void setPdbeNonObserved(int pdbeNonObserved2)
+    {
+      this.pdbeNonObserved = pdbeNonObserved2;
+    }
+
+    public int getPdbeNonObserved()
+    {
+      return pdbeNonObserved;
+    }
     public SequenceI getSeq()
     {
       return seq;
@@ -964,6 +1093,7 @@ public class SiftsClient implements SiftsClientI
     {
       this.nonObservedShiftIndex = nonObservedShiftIndex;
     }
+
   }
 
   @Override
diff --git a/test/jalview/analysis/AAFrequencyTest.java b/test/jalview/analysis/AAFrequencyTest.java
index 75fb39e..2b6c512 100644
--- a/test/jalview/analysis/AAFrequencyTest.java
+++ b/test/jalview/analysis/AAFrequencyTest.java
@@ -25,17 +25,27 @@ import static org.testng.AssertJUnit.assertNull;
 
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenMarkovModel;
+import jalview.datamodel.Profile;
 import jalview.datamodel.ProfileI;
+import jalview.datamodel.Profiles;
 import jalview.datamodel.ProfilesI;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
+import jalview.io.FileParse;
+import jalview.io.HMMFile;
+
+import java.io.IOException;
+import java.net.MalformedURLException;
 
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 public class AAFrequencyTest
 {
+  HiddenMarkovModel hmm;
 
   @BeforeClass(alwaysRun = true)
   public void setUpJvOptionPane()
@@ -44,6 +54,17 @@ public class AAFrequencyTest
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
   }
 
+  @BeforeClass(alwaysRun = true)
+  public void setUp() throws IOException, MalformedURLException
+  {
+    /*
+     * load a dna (ACGT) HMM file to a HiddenMarkovModel
+     */
+    HMMFile hmmFile = new HMMFile(new FileParse(
+            "test/jalview/io/test_MADE1_hmm.txt", DataSourceType.FILE));
+    hmm = hmmFile.getHMM();
+  }
+
   @Test(groups = { "Functional" })
   public void testCalculate_noProfile()
   {
@@ -232,4 +253,94 @@ public class AAFrequencyTest
     assertEquals("T 75%", ann.description);
     assertEquals("T", ann.displayCharacter);
   }
+
+  @Test(groups = { "Functional" })
+  public void testExtractHMMProfile()
+          throws MalformedURLException, IOException
+  {
+    int[] expected = { 0, 4, 100, 'T', 71, 'C', 12, 'G', 9, 'A', 9 };
+    int[] actual = AAFrequency.extractHMMProfile(hmm, 17, false, false);
+    for (int i = 0; i < actual.length; i++)
+    {
+      if (i == 2)
+      {
+        assertEquals(actual[i], expected[i]);
+      }
+      else
+      {
+        assertEquals(actual[i], expected[i]);
+      }
+    }
+
+    int[] expected2 = { 0, 4, 100, 'A', 85, 'C', 0, 'G', 0, 'T', 0 };
+    int[] actual2 = AAFrequency.extractHMMProfile(hmm, 2, true, false);
+    for (int i = 0; i < actual2.length; i++)
+    {
+      if (i == 2)
+      {
+        assertEquals(actual[i], expected[i]);
+      }
+      else
+      {
+        assertEquals(actual[i], expected[i]);
+      }
+    }
+
+    assertNull(AAFrequency.extractHMMProfile(null, 98978867, true, false));
+  }
+
+  @Test(groups = { "Functional" })
+  public void testGetAnalogueCount()
+  {
+    /*
+     * 'T' in column 0 has emission probability 0.7859, scales to 7859
+     */
+    int count = AAFrequency.getAnalogueCount(hmm, 0, 'T', false, false);
+    assertEquals(7859, count);
+
+    /*
+     * same with 'use info height': value is multiplied by log ratio
+     * log(value / background) / log(2) = log(0.7859/0.25)/0.693
+     * = log(3.1)/0.693 = 1.145/0.693 = 1.66
+     * so value becomes 1.2987 and scales up to 12987
+     */
+    count = AAFrequency.getAnalogueCount(hmm, 0, 'T', false, true);
+    assertEquals(12987, count);
+
+    /*
+     * 'G' in column 20 has emission probability 0.75457, scales to 7546
+     */
+    count = AAFrequency.getAnalogueCount(hmm, 20, 'G', false, false);
+    assertEquals(7546, count);
+
+    /*
+     * 'G' in column 1077 has emission probability 0.0533, here
+     * ignored (set to 0) since below background of 0.25
+     */
+    count = AAFrequency.getAnalogueCount(hmm, 1077, 'G', true, false);
+    assertEquals(0, count);
+  }
+
+  @Test(groups = { "Functional" })
+  public void testCompleteInformation()
+  {
+    ProfileI prof1 = new Profile(1, 0, 100, "A");
+    ProfileI prof2 = new Profile(1, 0, 100, "-");
+
+    ProfilesI profs = new Profiles(new ProfileI[] { prof1, prof2 });
+    Annotation ann1 = new Annotation(6.5f);
+    Annotation ann2 = new Annotation(0f);
+    Annotation[] annots = new Annotation[] { ann1, ann2 };
+    SequenceI seq = new Sequence("", "AA", 0, 0);
+    seq.setHMM(hmm);
+    AlignmentAnnotation annot = new AlignmentAnnotation("", "", annots);
+    annot.setSequenceRef(seq);
+    AAFrequency.completeInformation(annot, profs, 0, 1);
+    float ic = annot.annotations[0].value;
+    assertEquals(0.91532f, ic, 0.0001f);
+    ic = annot.annotations[1].value;
+    assertEquals(0f, ic, 0.0001f);
+    int i = 0;
+  }
+
 }
diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index 37b93fd..92bf0ce 100644
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -48,6 +48,7 @@ import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
 import jalview.io.FileFormatI;
 import jalview.io.FormatAdapter;
+import jalview.io.gff.SequenceOntologyI;
 import jalview.util.MapList;
 import jalview.util.MappingUtils;
 
@@ -2082,6 +2083,7 @@ public class AlignmentUtilsTests
     List<DnaVariant> codon1Variants = new ArrayList<>();
     List<DnaVariant> codon2Variants = new ArrayList<>();
     List<DnaVariant> codon3Variants = new ArrayList<>();
+
     List<DnaVariant> codonVariants[] = new ArrayList[3];
     codonVariants[0] = codon1Variants;
     codonVariants[1] = codon2Variants;
@@ -2734,7 +2736,7 @@ public class AlignmentUtilsTests
      * Case 2: CDS 3 times length of peptide + stop codon
      * (note code does not currently check trailing codon is a stop codon)
      */
-    dna = new Sequence("dna", "AACGacgtCTCCTTGA");
+    dna = new Sequence("dna", "AACGacgtCTCCTCCC");
     dna.createDatasetSequence();
     dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
     dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 16, null));
@@ -2747,17 +2749,42 @@ public class AlignmentUtilsTests
             Arrays.deepToString(ml.getFromRanges().toArray()));
 
     /*
-     * Case 3: CDS not 3 times length of peptide - no mapping is made
+     * Case 3: CDS longer than 3 * peptide + stop codon - no mapping is made
+     */
+    dna = new Sequence("dna", "AACGacgtCTCCTTGATCA");
+    dna.createDatasetSequence();
+    dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
+    dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 19, null));
+    ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
+    assertNull(ml);
+
+    /*
+     * Case 4: CDS shorter than 3 * peptide - no mapping is made
+     */
+    dna = new Sequence("dna", "AACGacgtCTCC");
+    dna.createDatasetSequence();
+    dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
+    dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 12, null));
+    ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
+    assertNull(ml);
+
+    /*
+     * Case 5: CDS 3 times length of peptide + part codon - mapping is truncated
      */
     dna = new Sequence("dna", "AACGacgtCTCCTTG");
     dna.createDatasetSequence();
     dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
     dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 15, null));
     ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
-    assertNull(ml);
+    assertEquals(3, ml.getFromRatio());
+    assertEquals(1, ml.getToRatio());
+    assertEquals("[[1, 3]]",
+            Arrays.deepToString(ml.getToRanges().toArray()));
+    assertEquals("[[1, 4], [9, 13]]",
+            Arrays.deepToString(ml.getFromRanges().toArray()));
 
     /*
-     * Case 4: incomplete start codon corresponding to X in peptide
+     * Case 6: incomplete start codon corresponding to X in peptide
      */
     dna = new Sequence("dna", "ACGacgtCTCCTTGG");
     dna.createDatasetSequence();
@@ -2772,4 +2799,152 @@ public class AlignmentUtilsTests
     assertEquals("[[3, 3], [8, 12]]",
             Arrays.deepToString(ml.getFromRanges().toArray()));
   }
+
+  /**
+   * Tests for the method that locates the CDS sequence that has a mapping to
+   * the given protein. That is, given a transcript-to-peptide mapping, find the
+   * cds-to-peptide mapping that relates to both, and return the CDS sequence.
+   */
+  @Test
+  public void testFindCdsForProtein()
+  {
+    List<AlignedCodonFrame> mappings = new ArrayList<>();
+    AlignedCodonFrame acf1 = new AlignedCodonFrame();
+    mappings.add(acf1);
+
+    SequenceI dna1 = new Sequence("dna1", "cgatATcgGCTATCTATGacg");
+    dna1.createDatasetSequence();
+
+    // NB we currently exclude STOP codon from CDS sequences
+    // the test would need to change if this changes in future
+    SequenceI cds1 = new Sequence("cds1", "ATGCTATCT");
+    cds1.createDatasetSequence();
+
+    SequenceI pep1 = new Sequence("pep1", "MLS");
+    pep1.createDatasetSequence();
+    List<AlignedCodonFrame> seqMappings = new ArrayList<>();
+    MapList mapList = new MapList(
+            new int[]
+            { 5, 6, 9, 15 }, new int[] { 1, 3 }, 3, 1);
+    Mapping dnaToPeptide = new Mapping(pep1.getDatasetSequence(), mapList);
+    
+    // add dna to peptide mapping
+    seqMappings.add(acf1);
+    acf1.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(),
+            mapList);
+
+    /*
+     * first case - no dna-to-CDS mapping exists - search fails
+     */
+    SequenceI seq = AlignmentUtils.findCdsForProtein(mappings, dna1,
+            seqMappings, dnaToPeptide);
+    assertNull(seq);
+
+    /*
+     * second case - CDS-to-peptide mapping exists but no dna-to-CDS
+     * - search fails
+     */
+    // todo this test fails if the mapping is added to acf1, not acf2
+    // need to tidy up use of lists of mappings in AlignedCodonFrame
+    AlignedCodonFrame acf2 = new AlignedCodonFrame();
+    mappings.add(acf2);
+    MapList cdsToPeptideMapping = new MapList(new int[]
+    { 1, 9 }, new int[] { 1, 3 }, 3, 1);
+    acf2.addMap(cds1.getDatasetSequence(), pep1.getDatasetSequence(),
+            cdsToPeptideMapping);
+    assertNull(AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
+            dnaToPeptide));
+
+    /*
+     * third case - add dna-to-CDS mapping - CDS is now found!
+     */
+    MapList dnaToCdsMapping = new MapList(new int[] { 5, 6, 9, 15 },
+            new int[]
+            { 1, 9 }, 1, 1);
+    acf1.addMap(dna1.getDatasetSequence(), cds1.getDatasetSequence(),
+            dnaToCdsMapping);
+    seq = AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
+            dnaToPeptide);
+    assertSame(seq, cds1.getDatasetSequence());
+  }
+
+  /**
+   * Tests for the method that locates the CDS sequence that has a mapping to
+   * the given protein. That is, given a transcript-to-peptide mapping, find the
+   * cds-to-peptide mapping that relates to both, and return the CDS sequence.
+   * This test is for the case where transcript and CDS are the same length.
+   */
+  @Test
+  public void testFindCdsForProtein_noUTR()
+  {
+    List<AlignedCodonFrame> mappings = new ArrayList<>();
+    AlignedCodonFrame acf1 = new AlignedCodonFrame();
+    mappings.add(acf1);
+  
+    SequenceI dna1 = new Sequence("dna1", "ATGCTATCTTAA");
+    dna1.createDatasetSequence();
+  
+    // NB we currently exclude STOP codon from CDS sequences
+    // the test would need to change if this changes in future
+    SequenceI cds1 = new Sequence("cds1", "ATGCTATCT");
+    cds1.createDatasetSequence();
+  
+    SequenceI pep1 = new Sequence("pep1", "MLS");
+    pep1.createDatasetSequence();
+    List<AlignedCodonFrame> seqMappings = new ArrayList<>();
+    MapList mapList = new MapList(
+            new int[]
+            { 1, 9 }, new int[] { 1, 3 }, 3, 1);
+    Mapping dnaToPeptide = new Mapping(pep1.getDatasetSequence(), mapList);
+    
+    // add dna to peptide mapping
+    seqMappings.add(acf1);
+    acf1.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(),
+            mapList);
+  
+    /*
+     * first case - transcript lacks CDS features - it appears to be
+     * the CDS sequence and is returned
+     */
+    SequenceI seq = AlignmentUtils.findCdsForProtein(mappings, dna1,
+            seqMappings, dnaToPeptide);
+    assertSame(seq, dna1.getDatasetSequence());
+  
+    /*
+     * second case - transcript has CDS feature - this means it is
+     * not returned as a match for CDS (CDS sequences don't have CDS features)
+     */
+    dna1.addSequenceFeature(
+            new SequenceFeature(SequenceOntologyI.CDS, "cds", 1, 12, null));
+    seq = AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
+            dnaToPeptide);
+    assertNull(seq);
+
+    /*
+     * third case - CDS-to-peptide mapping exists but no dna-to-CDS
+     * - search fails
+     */
+    // todo this test fails if the mapping is added to acf1, not acf2
+    // need to tidy up use of lists of mappings in AlignedCodonFrame
+    AlignedCodonFrame acf2 = new AlignedCodonFrame();
+    mappings.add(acf2);
+    MapList cdsToPeptideMapping = new MapList(new int[]
+    { 1, 9 }, new int[] { 1, 3 }, 3, 1);
+    acf2.addMap(cds1.getDatasetSequence(), pep1.getDatasetSequence(),
+            cdsToPeptideMapping);
+    assertNull(AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
+            dnaToPeptide));
+  
+    /*
+     * fourth case - add dna-to-CDS mapping - CDS is now found!
+     */
+    MapList dnaToCdsMapping = new MapList(new int[] { 1, 9 },
+            new int[]
+            { 1, 9 }, 1, 1);
+    acf1.addMap(dna1.getDatasetSequence(), cds1.getDatasetSequence(),
+            dnaToCdsMapping);
+    seq = AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
+            dnaToPeptide);
+    assertSame(seq, cds1.getDatasetSequence());
+  }
 }
diff --git a/test/jalview/analysis/CrossRefTest.java b/test/jalview/analysis/CrossRefTest.java
index 95be1ff..0265af3 100644
--- a/test/jalview/analysis/CrossRefTest.java
+++ b/test/jalview/analysis/CrossRefTest.java
@@ -106,7 +106,7 @@ public class CrossRefTest
   public void testFindXrefSourcesForSequence_proteinToDna()
   {
     SequenceI seq = new Sequence("Seq1", "MGKYQARLSS");
-    List<String> sources = new ArrayList<String>();
+    List<String> sources = new ArrayList<>();
     AlignmentI al = new Alignment(new SequenceI[] {});
 
     /*
@@ -132,8 +132,9 @@ public class CrossRefTest
     sources = new CrossRef(new SequenceI[] { seq }, al)
             .findXrefSourcesForSequences(false);
     // method is patched to remove EMBL from the sources to match
-    assertEquals(3, sources.size());
-    assertEquals("[EMBLCDS, GENEDB, ENSEMBL]", sources.toString());
+    assertEquals(4, sources.size());
+    assertEquals("[EMBLCDS, GENEDB, ENSEMBL, ENSEMBLGENOMES]",
+            sources.toString());
 
     /*
      * add a sequence to the alignment which has a dbref to UNIPROT|A1234
@@ -270,7 +271,7 @@ public class CrossRefTest
     pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2"));
     AlignmentI al = new Alignment(new SequenceI[] { dna1, pep1 });
 
-    List<SequenceI> result = new ArrayList<SequenceI>();
+    List<SequenceI> result = new ArrayList<>();
 
     /*
      * first search for a dbref nowhere on the alignment:
diff --git a/test/jalview/analysis/DnaTest.java b/test/jalview/analysis/DnaTest.java
index d2fa99a..6a31b31 100644
--- a/test/jalview/analysis/DnaTest.java
+++ b/test/jalview/analysis/DnaTest.java
@@ -38,6 +38,7 @@ import jalview.io.FileFormat;
 import jalview.io.FormatAdapter;
 
 import java.io.IOException;
+import java.util.Iterator;
 
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
@@ -135,7 +136,9 @@ public class DnaTest
             FileFormat.Fasta);
     HiddenColumns cs = new HiddenColumns();
     AlignViewportI av = new AlignViewport(alf, cs);
-    Dna dna = new Dna(av, new int[] { 0, alf.getWidth() - 1 });
+    Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
+            false);
+    Dna dna = new Dna(av, contigs);
     AlignmentI translated = dna.translateCdna();
     assertNotNull("Couldn't do a full width translation of test data.",
             translated);
@@ -163,7 +166,8 @@ public class DnaTest
         cs.hideColumns(0, ipos - 1);
       }
       cs.hideColumns(ipos + vwidth, alf.getWidth());
-      int[] vcontigs = cs.getVisibleContigs(0, alf.getWidth());
+      Iterator<int[]> vcontigs = cs.getVisContigsIterator(0,
+              alf.getWidth(), false);
       AlignViewportI av = new AlignViewport(alf, cs);
       Dna dna = new Dna(av, vcontigs);
       AlignmentI transAlf = dna.translateCdna();
@@ -190,7 +194,9 @@ public class DnaTest
             DataSourceType.PASTE, FileFormat.Fasta);
     HiddenColumns cs = new HiddenColumns();
     AlignViewportI av = new AlignViewport(alf, cs);
-    Dna dna = new Dna(av, new int[] { 0, alf.getWidth() - 1 });
+    Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
+            false);
+    Dna dna = new Dna(av, contigs);
     AlignmentI translated = dna.translateCdna();
     String aa = translated.getSequenceAt(0).getSequenceAsString();
     assertEquals(
@@ -213,7 +219,9 @@ public class DnaTest
     cs.hideColumns(24, 35); // hide codons 9-12
     cs.hideColumns(177, 191); // hide codons 60-64
     AlignViewportI av = new AlignViewport(alf, cs);
-    Dna dna = new Dna(av, new int[] { 0, alf.getWidth() - 1 });
+    Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
+            false);
+    Dna dna = new Dna(av, contigs);
     AlignmentI translated = dna.translateCdna();
     String aa = translated.getSequenceAt(0).getSequenceAsString();
     assertEquals("AACDDGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVW", aa);
@@ -298,7 +306,9 @@ public class DnaTest
             .generate(12, 8, 97, 5, 5);
     HiddenColumns cs = new HiddenColumns();
     AlignViewportI av = new AlignViewport(cdna, cs);
-    Dna dna = new Dna(av, new int[] { 0, cdna.getWidth() - 1 });
+    Iterator<int[]> contigs = cs.getVisContigsIterator(0, cdna.getWidth(),
+            false);
+    Dna dna = new Dna(av, contigs);
     AlignmentI translated = dna.translateCdna();
 
     /*
@@ -313,7 +323,8 @@ public class DnaTest
     }
     AlignmentI cdnaReordered = new Alignment(sorted);
     av = new AlignViewport(cdnaReordered, cs);
-    dna = new Dna(av, new int[] { 0, cdna.getWidth() - 1 });
+    contigs = cs.getVisContigsIterator(0, cdna.getWidth(), false);
+    dna = new Dna(av, contigs);
     AlignmentI translated2 = dna.translateCdna();
 
     /*
@@ -544,7 +555,9 @@ public class DnaTest
 
     HiddenColumns cs = new HiddenColumns();
     AlignViewportI av = new AlignViewport(al, cs);
-    Dna testee = new Dna(av, new int[] { 0, al.getWidth() - 1 });
+    Iterator<int[]> contigs = cs.getVisContigsIterator(0, al.getWidth(),
+            false);
+    Dna testee = new Dna(av, contigs);
     AlignmentI reversed = testee.reverseCdna(false);
     assertEquals(1, reversed.getHeight());
     assertEquals(seqRev, reversed.getSequenceAt(0).getSequenceAsString());
diff --git a/test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java b/test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java
index 16ca70d..a1623f6 100644
--- a/test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java
+++ b/test/jalview/analysis/scoremodels/FeatureDistanceModelTest.java
@@ -23,6 +23,7 @@ package jalview.analysis.scoremodels;
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertTrue;
 
+import jalview.api.AlignViewportI;
 import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.SimilarityParamsI;
 import jalview.datamodel.Alignment;
@@ -32,7 +33,6 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
-import jalview.gui.AlignViewport;
 import jalview.gui.JvOptionPane;
 import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
@@ -280,7 +280,7 @@ public class FeatureDistanceModelTest
   public void testFindDistances_withParams()
   {
     AlignFrame af = setupAlignmentView();
-    AlignViewport viewport = af.getViewport();
+    AlignViewportI viewport = af.getViewport();
     AlignmentView view = viewport.getAlignmentView(false);
 
     ScoreModelI sm = new FeatureDistanceModel();
diff --git a/test/jalview/datamodel/AlignmentAnnotationTests.java b/test/jalview/datamodel/AlignmentAnnotationTests.java
index e47e9d6..19a725e 100644
--- a/test/jalview/datamodel/AlignmentAnnotationTests.java
+++ b/test/jalview/datamodel/AlignmentAnnotationTests.java
@@ -20,8 +20,8 @@
  */
 package jalview.datamodel;
 
+import static org.testng.Assert.assertNull;
 import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertNull;
 
 import jalview.analysis.AlignSeq;
 import jalview.gui.JvOptionPane;
@@ -335,4 +335,92 @@ public class AlignmentAnnotationTests
     Assert.assertTrue(ann.isQuantitative(),
             "Mixed 'E' annotation set should be quantitative.");
   }
+
+  @Test(groups = "Functional")
+  public void testMakeVisibleAnnotation()
+  {
+    HiddenColumns h = new HiddenColumns();
+    Annotation[] anns = new Annotation[] { null, null, new Annotation(1),
+        new Annotation(2), new Annotation(3), null, null, new Annotation(4),
+        new Annotation(5), new Annotation(6), new Annotation(7),
+        new Annotation(8) };
+    AlignmentAnnotation ann = new AlignmentAnnotation("an", "some an",
+            anns);
+
+    // null annotations
+    AlignmentAnnotation emptyann = new AlignmentAnnotation("an", "some ann",
+            null);
+    emptyann.makeVisibleAnnotation(h);
+    assertNull(emptyann.annotations);
+
+    emptyann.makeVisibleAnnotation(3, 4, h);
+    assertNull(emptyann.annotations);
+
+    // without bounds, does everything
+    ann.makeVisibleAnnotation(h);
+    assertEquals(12, ann.annotations.length);
+    assertNull(ann.annotations[0]);
+    assertNull(ann.annotations[1]);
+    assertEquals(1.0f, ann.annotations[2].value);
+    assertEquals(2.0f, ann.annotations[3].value);
+    assertEquals(3.0f, ann.annotations[4].value);
+    assertNull(ann.annotations[5]);
+    assertNull(ann.annotations[6]);
+    assertEquals(4.0f, ann.annotations[7].value);
+    assertEquals(5.0f, ann.annotations[8].value);
+    assertEquals(6.0f, ann.annotations[9].value);
+    assertEquals(7.0f, ann.annotations[10].value);
+    assertEquals(8.0f, ann.annotations[11].value);
+
+    // without hidden cols, just truncates
+    ann.makeVisibleAnnotation(3, 5, h);
+    assertEquals(3, ann.annotations.length);
+    assertEquals(2.0f, ann.annotations[0].value);
+    assertEquals(3.0f, ann.annotations[1].value);
+    assertNull(ann.annotations[2]);
+
+    anns = new Annotation[] { null, null, new Annotation(1),
+        new Annotation(2), new Annotation(3), null, null, new Annotation(4),
+        new Annotation(5), new Annotation(6), new Annotation(7),
+        new Annotation(8) };
+    ann = new AlignmentAnnotation("an", "some an", anns);
+    h.hideColumns(4, 7);
+    ann.makeVisibleAnnotation(1, 9, h);
+    assertEquals(5, ann.annotations.length);
+    assertNull(ann.annotations[0]);
+    assertEquals(1.0f, ann.annotations[1].value);
+    assertEquals(2.0f, ann.annotations[2].value);
+    assertEquals(5.0f, ann.annotations[3].value);
+    assertEquals(6.0f, ann.annotations[4].value);
+
+    anns = new Annotation[] { null, null, new Annotation(1),
+        new Annotation(2), new Annotation(3), null, null, new Annotation(4),
+        new Annotation(5), new Annotation(6), new Annotation(7),
+        new Annotation(8) };
+    ann = new AlignmentAnnotation("an", "some an", anns);
+    h.hideColumns(1, 2);
+    ann.makeVisibleAnnotation(1, 9, h);
+    assertEquals(3, ann.annotations.length);
+    assertEquals(2.0f, ann.annotations[0].value);
+    assertEquals(5.0f, ann.annotations[1].value);
+    assertEquals(6.0f, ann.annotations[2].value);
+
+    anns = new Annotation[] { null, null, new Annotation(1),
+        new Annotation(2), new Annotation(3), null, null, new Annotation(4),
+        new Annotation(5), new Annotation(6), new Annotation(7),
+        new Annotation(8), new Annotation(9), new Annotation(10),
+        new Annotation(11), new Annotation(12), new Annotation(13),
+        new Annotation(14), new Annotation(15) };
+    ann = new AlignmentAnnotation("an", "some an", anns);
+    h = new HiddenColumns();
+    h.hideColumns(5, 18);
+    h.hideColumns(20, 21);
+    ann.makeVisibleAnnotation(1, 21, h);
+    assertEquals(5, ann.annotations.length);
+    assertEquals(1.0f, ann.annotations[1].value);
+    assertEquals(2.0f, ann.annotations[2].value);
+    assertEquals(3.0f, ann.annotations[3].value);
+    assertNull(ann.annotations[0]);
+    assertNull(ann.annotations[4]);
+  }
 }
diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index 4b5d096..0f6b129 100644
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@ -34,6 +34,7 @@ import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
 import jalview.io.FileFormatI;
 import jalview.io.FormatAdapter;
+import jalview.util.Comparison;
 import jalview.util.MapList;
 
 import java.io.IOException;
@@ -247,7 +248,9 @@ public class AlignmentTest
                   if (raiseAssert)
                   {
                     Assert.fail(message
-                            + " DBRefEntry for sequence in alignment had map to sequence not in dataset");
+                            + " DBRefEntry " + dbr + " for sequence "
+                            + seqds
+                            + " in alignment has map to sequence not in dataset");
                   }
                   return false;
                 }
@@ -668,6 +671,17 @@ public class AlignmentTest
     // third found.. so
     assertFalse(iter.hasNext());
 
+    // search for annotation on one sequence with a particular label - expect
+    // one
+    SequenceI sqfound;
+    anns = al.findAnnotations(sqfound = al.getSequenceAt(1), null,
+            "Secondary Structure");
+    iter = anns.iterator();
+    assertTrue(iter.hasNext());
+    // expect reference to sequence 1 in the alignment
+    assertTrue(sqfound == iter.next().sequenceRef);
+    assertFalse(iter.hasNext());
+
     // null on all parameters == find all annotations
     anns = al.findAnnotations(null, null, null);
     iter = anns.iterator();
@@ -1321,4 +1335,153 @@ public class AlignmentTest
     // todo test coverage for annotations, mappings, groups,
     // hidden sequences, properties
   }
+
+  /**
+   * test that calcId == null on findOrCreate doesn't raise an NPE, and yields
+   * an annotation with a null calcId
+   * 
+   */
+  @Test(groups = "Functional")
+  public void testFindOrCreateForNullCalcId()
+  {
+    SequenceI seq = new Sequence("seq1", "FRMLPSRT-A--L-");
+    AlignmentI alignment = new Alignment(new SequenceI[] { seq });
+
+    AlignmentAnnotation ala = alignment.findOrCreateAnnotation(
+            "Temperature Factor", null, false, seq, null);
+    assertNotNull(ala);
+    assertEquals(seq, ala.sequenceRef);
+    assertEquals("", ala.getCalcId());
+  }
+
+  @Test(groups = "Functional")
+  public void testPropagateInsertions()
+  {
+    // create an alignment with no gaps - this will be the profile seq and other
+    // JPRED seqs
+    AlignmentGenerator gen = new AlignmentGenerator(false);
+    AlignmentI al = gen.generate(25, 10, 1234, 0, 0);
+
+    // get the profileseq
+    SequenceI profileseq = al.getSequenceAt(0);
+    SequenceI gappedseq = new Sequence(profileseq);
+    gappedseq.insertCharAt(5, al.getGapCharacter());
+    gappedseq.insertCharAt(6, al.getGapCharacter());
+    gappedseq.insertCharAt(7, al.getGapCharacter());
+    gappedseq.insertCharAt(8, al.getGapCharacter());
+
+    // force different kinds of padding
+    al.getSequenceAt(3).deleteChars(2, 23);
+    al.getSequenceAt(4).deleteChars(2, 27);
+    al.getSequenceAt(5).deleteChars(10, 27);
+
+    // create an alignment view with the gapped sequence
+    SequenceI[] seqs = new SequenceI[1];
+    seqs[0] = gappedseq;
+    AlignmentI newal = new Alignment(seqs);
+    HiddenColumns hidden = new HiddenColumns();
+    hidden.hideColumns(15, 17);
+
+    AlignmentView view = new AlignmentView(newal, hidden, null, true, false,
+            false);
+
+    // confirm that original contigs are as expected
+    Iterator<int[]> visible = hidden.getVisContigsIterator(0, 25, false);
+    int[] region = visible.next();
+    assertEquals("[0, 14]", Arrays.toString(region));
+    region = visible.next();
+    assertEquals("[18, 24]", Arrays.toString(region));
+
+    // propagate insertions
+    HiddenColumns result = al.propagateInsertions(profileseq, view);
+
+    // confirm that the contigs have changed to account for the gaps
+    visible = result.getVisContigsIterator(0, 25, false);
+    region = visible.next();
+    assertEquals("[0, 10]", Arrays.toString(region));
+    region = visible.next();
+    assertEquals("[14, 24]", Arrays.toString(region));
+
+    // confirm the alignment has been changed so that the other sequences have
+    // gaps inserted where the columns are hidden
+    assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[10]));
+    assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[11]));
+    assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[12]));
+    assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[13]));
+    assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[14]));
+
+  }
+
+  @Test(groups = "Functional")
+  public void testPropagateInsertionsOverlap()
+  {
+    // test propagateInsertions where gaps and hiddenColumns overlap
+
+    // create an alignment with no gaps - this will be the profile seq and other
+    // JPRED seqs
+    AlignmentGenerator gen = new AlignmentGenerator(false);
+    AlignmentI al = gen.generate(20, 10, 1234, 0, 0);
+
+    // get the profileseq
+    SequenceI profileseq = al.getSequenceAt(0);
+    SequenceI gappedseq = new Sequence(profileseq);
+    gappedseq.insertCharAt(5, al.getGapCharacter());
+    gappedseq.insertCharAt(6, al.getGapCharacter());
+    gappedseq.insertCharAt(7, al.getGapCharacter());
+    gappedseq.insertCharAt(8, al.getGapCharacter());
+
+    // create an alignment view with the gapped sequence
+    SequenceI[] seqs = new SequenceI[1];
+    seqs[0] = gappedseq;
+    AlignmentI newal = new Alignment(seqs);
+
+    // hide columns so that some overlap with the gaps
+    HiddenColumns hidden = new HiddenColumns();
+    hidden.hideColumns(7, 10);
+
+    AlignmentView view = new AlignmentView(newal, hidden, null, true, false,
+            false);
+
+    // confirm that original contigs are as expected
+    Iterator<int[]> visible = hidden.getVisContigsIterator(0, 20, false);
+    int[] region = visible.next();
+    assertEquals("[0, 6]", Arrays.toString(region));
+    region = visible.next();
+    assertEquals("[11, 19]", Arrays.toString(region));
+    assertFalse(visible.hasNext());
+
+    // propagate insertions
+    HiddenColumns result = al.propagateInsertions(profileseq, view);
+
+    // confirm that the contigs have changed to account for the gaps
+    visible = result.getVisContigsIterator(0, 20, false);
+    region = visible.next();
+    assertEquals("[0, 4]", Arrays.toString(region));
+    region = visible.next();
+    assertEquals("[7, 19]", Arrays.toString(region));
+    assertFalse(visible.hasNext());
+
+    // confirm the alignment has been changed so that the other sequences have
+    // gaps inserted where the columns are hidden
+    assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[4]));
+    assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[5]));
+    assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[6]));
+    assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[7]));
+  }
+
+  @Test(groups = { "Functional" })
+  public void testPadGaps()
+  {
+    SequenceI seq1 = new Sequence("seq1", "ABCDEF--");
+    SequenceI seq2 = new Sequence("seq2", "-JKLMNO--");
+    SequenceI seq3 = new Sequence("seq2", "-PQR");
+    AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
+    a.setGapCharacter('.'); // this replaces existing gaps
+    assertEquals("ABCDEF..", seq1.getSequenceAsString());
+    a.padGaps();
+    // trailing gaps are pruned, short sequences padded with gap character
+    assertEquals("ABCDEF.", seq1.getSequenceAsString());
+    assertEquals(".JKLMNO", seq2.getSequenceAsString());
+    assertEquals(".PQR...", seq3.getSequenceAsString());
+  }
 }
diff --git a/test/jalview/datamodel/AlignmentViewTest.java b/test/jalview/datamodel/AlignmentViewTest.java
index b201c7e..9be344c 100644
--- a/test/jalview/datamodel/AlignmentViewTest.java
+++ b/test/jalview/datamodel/AlignmentViewTest.java
@@ -23,10 +23,10 @@ package jalview.datamodel;
 import static org.testng.Assert.assertEquals;
 
 import jalview.gui.AlignFrame;
-import jalview.gui.AlignViewport;
 import jalview.gui.JvOptionPane;
 import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
+import jalview.viewmodel.AlignmentViewport;
 
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
@@ -60,7 +60,7 @@ public class AlignmentViewTest
   {
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             ">s1\n0123456789\n", DataSourceType.PASTE);
-    AlignViewport av = af.getViewport();
+    AlignmentViewport av = af.getViewport();
     AlignmentView view = av.getAlignmentView(true);
 
     /*
diff --git a/test/jalview/datamodel/ColumnSelectionTest.java b/test/jalview/datamodel/ColumnSelectionTest.java
index e99e952..8709961 100644
--- a/test/jalview/datamodel/ColumnSelectionTest.java
+++ b/test/jalview/datamodel/ColumnSelectionTest.java
@@ -32,6 +32,7 @@ import java.util.Arrays;
 import java.util.BitSet;
 import java.util.Collections;
 import java.util.ConcurrentModificationException;
+import java.util.Iterator;
 import java.util.List;
 
 import org.testng.annotations.BeforeClass;
@@ -132,9 +133,9 @@ public class ColumnSelectionTest
     // hide column 5 (and adjacent):
     cs.hideSelectedColumns(5, al.getHiddenColumns());
     // 4,5,6 now hidden:
-    List<int[]> hidden = al.getHiddenColumns().getHiddenColumnsCopy();
-    assertEquals(1, hidden.size());
-    assertEquals("[4, 6]", Arrays.toString(hidden.get(0)));
+    Iterator<int[]> regions = al.getHiddenColumns().iterator();
+    assertEquals(1, al.getHiddenColumns().getNumberOfRegions());
+    assertEquals("[4, 6]", Arrays.toString(regions.next()));
     // none now selected:
     assertTrue(cs.getSelected().isEmpty());
 
@@ -145,9 +146,9 @@ public class ColumnSelectionTest
     cs.addElement(5);
     cs.addElement(6);
     cs.hideSelectedColumns(4, al.getHiddenColumns());
-    hidden = al.getHiddenColumns().getHiddenColumnsCopy();
-    assertEquals(1, hidden.size());
-    assertEquals("[4, 6]", Arrays.toString(hidden.get(0)));
+    regions = al.getHiddenColumns().iterator();
+    assertEquals(1, al.getHiddenColumns().getNumberOfRegions());
+    assertEquals("[4, 6]", Arrays.toString(regions.next()));
     assertTrue(cs.getSelected().isEmpty());
 
     // repeat, hiding column (4, 5 and) 6
@@ -157,9 +158,9 @@ public class ColumnSelectionTest
     cs.addElement(5);
     cs.addElement(6);
     cs.hideSelectedColumns(6, al.getHiddenColumns());
-    hidden = al.getHiddenColumns().getHiddenColumnsCopy();
-    assertEquals(1, hidden.size());
-    assertEquals("[4, 6]", Arrays.toString(hidden.get(0)));
+    regions = al.getHiddenColumns().iterator();
+    assertEquals(1, al.getHiddenColumns().getNumberOfRegions());
+    assertEquals("[4, 6]", Arrays.toString(regions.next()));
     assertTrue(cs.getSelected().isEmpty());
 
     // repeat, with _only_ adjacent columns selected
@@ -168,9 +169,9 @@ public class ColumnSelectionTest
     cs.addElement(4);
     cs.addElement(6);
     cs.hideSelectedColumns(5, al.getHiddenColumns());
-    hidden = al.getHiddenColumns().getHiddenColumnsCopy();
-    assertEquals(1, hidden.size());
-    assertEquals("[4, 6]", Arrays.toString(hidden.get(0)));
+    regions = al.getHiddenColumns().iterator();
+    assertEquals(1, al.getHiddenColumns().getNumberOfRegions());
+    assertEquals("[4, 6]", Arrays.toString(regions.next()));
     assertTrue(cs.getSelected().isEmpty());
   }
 
@@ -196,12 +197,12 @@ public class ColumnSelectionTest
 
     cs.hideSelectedColumns(al);
     assertTrue(cs.getSelected().isEmpty());
-    List<int[]> hidden = cols.getHiddenColumnsCopy();
-    assertEquals(4, hidden.size());
-    assertEquals("[2, 4]", Arrays.toString(hidden.get(0)));
-    assertEquals("[7, 9]", Arrays.toString(hidden.get(1)));
-    assertEquals("[15, 18]", Arrays.toString(hidden.get(2)));
-    assertEquals("[20, 22]", Arrays.toString(hidden.get(3)));
+    Iterator<int[]> regions = cols.iterator();
+    assertEquals(4, cols.getNumberOfRegions());
+    assertEquals("[2, 4]", Arrays.toString(regions.next()));
+    assertEquals("[7, 9]", Arrays.toString(regions.next()));
+    assertEquals("[15, 18]", Arrays.toString(regions.next()));
+    assertEquals("[20, 22]", Arrays.toString(regions.next()));
   }
 
   /**
diff --git a/test/jalview/datamodel/HMMNodeTest.java b/test/jalview/datamodel/HMMNodeTest.java
new file mode 100644
index 0000000..f2aef06
--- /dev/null
+++ b/test/jalview/datamodel/HMMNodeTest.java
@@ -0,0 +1,42 @@
+package jalview.datamodel;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.io.DataSourceType;
+import jalview.io.FileParse;
+import jalview.io.HMMFile;
+
+import java.io.IOException;
+import java.net.MalformedURLException;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+public class HMMNodeTest
+{
+  private HiddenMarkovModel hmm;
+
+  @BeforeClass(alwaysRun = true)
+  public void setUp() throws MalformedURLException, IOException
+  {
+    /*
+     * load hmm model of a Kinase domain to a HiddenMarkovModel
+     */
+    HMMFile file = new HMMFile(new FileParse(
+            "test/jalview/io/test_PKinase_hmm.txt", DataSourceType.FILE));
+    hmm = file.getHMM();
+  }
+
+  @Test(groups="Functional")
+  public void testGetMaxMatchEmissionIdex()
+  {
+    assertEquals(hmm.getAlphabetType(), "amino");
+    String symbols = hmm.getSymbols();
+
+    assertEquals(hmm.getNode(1).getMaxMatchEmissionIndex(),
+            symbols.indexOf('Y'));
+
+    assertEquals(hmm.getNode(17).getMaxMatchEmissionIndex(),
+            symbols.indexOf('K'));
+  }
+}
diff --git a/test/jalview/datamodel/HiddenColumnsCursorTest.java b/test/jalview/datamodel/HiddenColumnsCursorTest.java
new file mode 100644
index 0000000..97402b8
--- /dev/null
+++ b/test/jalview/datamodel/HiddenColumnsCursorTest.java
@@ -0,0 +1,157 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.datamodel;
+
+import static org.testng.Assert.assertNull;
+import static org.testng.AssertJUnit.assertEquals;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.testng.annotations.Test;
+
+public class HiddenColumnsCursorTest
+{
+
+  @Test(groups = { "Functional" })
+  public void testConstructor()
+  {
+    HiddenColumnsCursor cursor = new HiddenColumnsCursor();
+    assertNull(cursor.findRegionForColumn(0, false));
+
+    List<int[]> hlist = new ArrayList<>();
+    cursor = new HiddenColumnsCursor(hlist);
+    assertNull(cursor.findRegionForColumn(0, false));
+
+    cursor = new HiddenColumnsCursor(hlist, 3, 12);
+    assertNull(cursor.findRegionForColumn(0, false));
+
+    hlist.add(new int[] { 3, 7 });
+    hlist.add(new int[] { 15, 25 });
+    cursor = new HiddenColumnsCursor(hlist);
+    HiddenCursorPosition p = cursor.findRegionForColumn(8, false);
+    assertEquals(1, p.getRegionIndex());
+
+    cursor = new HiddenColumnsCursor(hlist, 1, 5);
+    p = cursor.findRegionForColumn(8, false);
+    assertEquals(1, p.getRegionIndex());
+  }
+
+  /**
+   * Test the method which finds the corresponding region given a column
+   */
+  @Test(groups = { "Functional" })
+  public void testFindRegionForColumn()
+  {
+    HiddenColumnsCursor cursor = new HiddenColumnsCursor();
+    
+    HiddenCursorPosition pos = cursor.findRegionForColumn(20, false);
+    assertNull(pos);
+    
+    List<int[]> hidden = new ArrayList<>();
+    hidden.add(new int[] { 53, 76 });
+    hidden.add(new int[] { 104, 125 });
+
+    cursor = new HiddenColumnsCursor(hidden);
+
+    int regionIndex = cursor.findRegionForColumn(126, false).getRegionIndex();
+    assertEquals(2, regionIndex);
+
+    regionIndex = cursor.findRegionForColumn(125, false).getRegionIndex();
+    assertEquals(1, regionIndex);
+
+    regionIndex = cursor.findRegionForColumn(108, false).getRegionIndex();
+    assertEquals(1, regionIndex);
+
+    regionIndex = cursor.findRegionForColumn(104, false).getRegionIndex();
+    assertEquals(1, regionIndex);
+
+    regionIndex = cursor.findRegionForColumn(103, false).getRegionIndex();
+    assertEquals(1, regionIndex);
+
+    regionIndex = cursor.findRegionForColumn(77, false).getRegionIndex();
+    assertEquals(1, regionIndex);
+
+    regionIndex = cursor.findRegionForColumn(76, false).getRegionIndex();
+    assertEquals(0, regionIndex);
+
+    regionIndex = cursor.findRegionForColumn(53, false).getRegionIndex();
+    assertEquals(0, regionIndex);
+
+    regionIndex = cursor.findRegionForColumn(52, false).getRegionIndex();
+    assertEquals(0, regionIndex);
+
+    regionIndex = cursor.findRegionForColumn(0, false).getRegionIndex();
+    assertEquals(0, regionIndex);
+
+    hidden.add(new int[] { 138, 155 });
+
+    cursor = new HiddenColumnsCursor(hidden);
+
+    regionIndex = cursor.findRegionForColumn(160, false).getRegionIndex();
+    assertEquals(3, regionIndex);
+
+    regionIndex = cursor.findRegionForColumn(100, false).getRegionIndex();
+    assertEquals(1, regionIndex);
+  }
+
+  /**
+   * Test the method which counts the number of hidden columns before a column
+   */
+  @Test(groups = { "Functional" })
+  public void testFindRegionForColumn_Visible()
+  {
+    HiddenColumnsCursor cursor = new HiddenColumnsCursor();
+
+    HiddenCursorPosition pos = cursor.findRegionForColumn(20, true);
+    assertNull(pos);
+
+    List<int[]> hidden = new ArrayList<>();
+    hidden.add(new int[] { 53, 76 });
+    hidden.add(new int[] { 104, 125 });
+
+    cursor = new HiddenColumnsCursor(hidden);
+
+    int offset = cursor.findRegionForColumn(80, true).getHiddenSoFar();
+    assertEquals(46, offset);
+
+    offset = cursor.findRegionForColumn(79, true).getHiddenSoFar();
+    assertEquals(24, offset);
+
+    offset = cursor.findRegionForColumn(53, true).getHiddenSoFar();
+    assertEquals(24, offset);
+
+    offset = cursor.findRegionForColumn(52, true).getHiddenSoFar();
+    assertEquals(0, offset);
+
+    offset = cursor.findRegionForColumn(10, true).getHiddenSoFar();
+    assertEquals(0, offset);
+
+    offset = cursor.findRegionForColumn(0, true).getHiddenSoFar();
+    assertEquals(0, offset);
+
+    offset = cursor.findRegionForColumn(79, true).getHiddenSoFar();
+    assertEquals(24, offset);
+
+    offset = cursor.findRegionForColumn(80, true).getHiddenSoFar();
+    assertEquals(46, offset);
+  }
+}
diff --git a/test/jalview/datamodel/HiddenColumnsTest.java b/test/jalview/datamodel/HiddenColumnsTest.java
index 7c88d71..2916199 100644
--- a/test/jalview/datamodel/HiddenColumnsTest.java
+++ b/test/jalview/datamodel/HiddenColumnsTest.java
@@ -26,26 +26,15 @@ import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.analysis.AlignmentGenerator;
-import jalview.gui.JvOptionPane;
 
 import java.util.Arrays;
 import java.util.BitSet;
-import java.util.List;
-import java.util.Random;
+import java.util.Iterator;
 
-import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 public class HiddenColumnsTest
 {
-
-  @BeforeClass(alwaysRun = true)
-  public void setUpJvOptionPane()
-  {
-    JvOptionPane.setInteractiveMode(false);
-    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
-  }
-
   /**
    * Test the method which counts the number of hidden columns
    */
@@ -77,22 +66,22 @@ public class HiddenColumnsTest
   public void testFindColumnPosition()
   {
     HiddenColumns cs = new HiddenColumns();
-    assertEquals(5, cs.findColumnPosition(5));
+    assertEquals(5, cs.absoluteToVisibleColumn(5));
 
     // hiding column 6 makes no difference
     cs.hideColumns(6, 6);
-    assertEquals(5, cs.findColumnPosition(5));
+    assertEquals(5, cs.absoluteToVisibleColumn(5));
 
     // hiding column 4 moves column 5 to column 4
     cs.hideColumns(4, 4);
-    assertEquals(4, cs.findColumnPosition(5));
+    assertEquals(4, cs.absoluteToVisibleColumn(5));
 
     // hiding column 4 moves column 4 to position 3
-    assertEquals(3, cs.findColumnPosition(4));
+    assertEquals(3, cs.absoluteToVisibleColumn(4));
 
     // hiding columns 1 and 2 moves column 5 to column 2
     cs.hideColumns(1, 2);
-    assertEquals(2, cs.findColumnPosition(5));
+    assertEquals(2, cs.absoluteToVisibleColumn(5));
 
     // check with > 1 hidden column regions
     // where some columns are in the hidden regions
@@ -102,105 +91,82 @@ public class HiddenColumnsTest
     cs2.hideColumns(40, 44);
 
     // hiding columns 5-10 and 20-27 moves column 8 to column 4
-    assertEquals(4, cs2.findColumnPosition(8));
+    assertEquals(4, cs2.absoluteToVisibleColumn(8));
 
     // and moves column 24 to 13
-    assertEquals(13, cs2.findColumnPosition(24));
+    assertEquals(13, cs2.absoluteToVisibleColumn(24));
 
     // and moves column 28 to 14
-    assertEquals(14, cs2.findColumnPosition(28));
+    assertEquals(14, cs2.absoluteToVisibleColumn(28));
 
     // and moves column 40 to 25
-    assertEquals(25, cs2.findColumnPosition(40));
+    assertEquals(25, cs2.absoluteToVisibleColumn(40));
 
     // check when hidden columns start at 0 that the visible column
     // is returned as 0
     HiddenColumns cs3 = new HiddenColumns();
     cs3.hideColumns(0, 4);
-    assertEquals(0, cs3.findColumnPosition(2));
+    assertEquals(0, cs3.absoluteToVisibleColumn(2));
 
+    // check that column after the last hidden region doesn't crash
+    assertEquals(46, cs2.absoluteToVisibleColumn(65));
   }
 
-  /**
-   * Test the method that finds the visible column position a given distance
-   * before another column
-   */
   @Test(groups = { "Functional" })
-  public void testFindColumnNToLeft()
+  public void testVisibleContigsIterator()
   {
     HiddenColumns cs = new HiddenColumns();
 
-    // test that without hidden columns, findColumnNToLeft returns
-    // position n to left of provided position
-    int pos = cs.subtractVisibleColumns(3, 10);
-    assertEquals(7, pos);
-
-    // 0 returns same position
-    pos = cs.subtractVisibleColumns(0, 10);
-    assertEquals(10, pos);
-
-    // overflow to left returns negative number
-    pos = cs.subtractVisibleColumns(3, 0);
-    assertEquals(-3, pos);
-
-    // test that with hidden columns to left of result column
-    // behaviour is the same as above
-    cs.hideColumns(1, 3);
-
-    // position n to left of provided position
-    pos = cs.subtractVisibleColumns(3, 10);
-    assertEquals(7, pos);
-
-    // 0 returns same position
-    pos = cs.subtractVisibleColumns(0, 10);
-    assertEquals(10, pos);
-
-    // test with one set of hidden columns between start and required position
-    cs.hideColumns(12, 15);
-    pos = cs.subtractVisibleColumns(8, 17);
-    assertEquals(5, pos);
-
-    // test with two sets of hidden columns between start and required position
-    cs.hideColumns(20, 21);
-    pos = cs.subtractVisibleColumns(8, 23);
-    assertEquals(9, pos);
-
-    // repeat last 2 tests with no hidden columns to left of required position
-    ColumnSelection colsel = new ColumnSelection();
-    cs.revealAllHiddenColumns(colsel);
-
-    // test with one set of hidden columns between start and required position
-    cs.hideColumns(12, 15);
-    pos = cs.subtractVisibleColumns(8, 17);
-    assertEquals(5, pos);
-
-    // test with two sets of hidden columns between start and required position
-    cs.hideColumns(20, 21);
-    pos = cs.subtractVisibleColumns(8, 23);
-    assertEquals(9, pos);
-
-  }
+    Iterator<int[]> visible = cs.getVisContigsIterator(3, 10, false);
+    int[] region = visible.next();
+    assertEquals("[3, 9]", Arrays.toString(region));
+    assertFalse(visible.hasNext());
 
-  @Test(groups = { "Functional" })
-  public void testGetVisibleContigs()
-  {
-    HiddenColumns cs = new HiddenColumns();
     cs.hideColumns(3, 6);
     cs.hideColumns(8, 9);
     cs.hideColumns(12, 12);
 
-    // start position is inclusive, end position exclusive:
-    int[] visible = cs.getVisibleContigs(1, 13);
-    assertEquals("[1, 2, 7, 7, 10, 11]", Arrays.toString(visible));
-
-    visible = cs.getVisibleContigs(4, 14);
-    assertEquals("[7, 7, 10, 11, 13, 13]", Arrays.toString(visible));
-
-    visible = cs.getVisibleContigs(3, 10);
-    assertEquals("[7, 7]", Arrays.toString(visible));
-
-    visible = cs.getVisibleContigs(4, 6);
-    assertEquals("[]", Arrays.toString(visible));
+    // Test both ends visible region
+
+    // start position is inclusive, end position exclusive
+    visible = cs.getVisContigsIterator(1, 13, false);
+    region = visible.next();
+    assertEquals("[1, 2]", Arrays.toString(region));
+    region = visible.next();
+    assertEquals("[7, 7]", Arrays.toString(region));
+    region = visible.next();
+    assertEquals("[10, 11]", Arrays.toString(region));
+    assertFalse(visible.hasNext());
+
+    // Test start hidden, end visible
+    visible = cs.getVisContigsIterator(4, 14, false);
+    region = visible.next();
+    assertEquals("[7, 7]", Arrays.toString(region));
+    region = visible.next();
+    assertEquals("[10, 11]", Arrays.toString(region));
+    region = visible.next();
+    assertEquals("[13, 13]", Arrays.toString(region));
+    assertFalse(visible.hasNext());
+
+    // Test start hidden, end hidden
+    visible = cs.getVisContigsIterator(3, 10, false);
+    region = visible.next();
+    assertEquals("[7, 7]", Arrays.toString(region));
+    assertFalse(visible.hasNext());
+
+    // Test start visible, end hidden
+    visible = cs.getVisContigsIterator(0, 13, false);
+    region = visible.next();
+    assertEquals("[0, 2]", Arrays.toString(region));
+    region = visible.next();
+    assertEquals("[7, 7]", Arrays.toString(region));
+    region = visible.next();
+    assertEquals("[10, 11]", Arrays.toString(region));
+    assertFalse(visible.hasNext());
+
+    // Test empty result
+    visible = cs.getVisContigsIterator(4, 6, false);
+    assertFalse(visible.hasNext());
   }
 
   @Test(groups = { "Functional" })
@@ -216,14 +182,31 @@ public class HiddenColumnsTest
     assertFalse(cs.equals(cs2));
     assertFalse(cs2.equals(cs));
 
+    // with the wrong kind of object
+    assertFalse(cs.equals(new HiddenColumnsCursor()));
+
+    // with a different hiddenColumns object - by size
+    HiddenColumns cs3 = new HiddenColumns();
+    cs3.hideColumns(2, 3);
+    assertFalse(cs.equals(cs3));
+
     // with hidden columns added in a different order
     cs2.hideColumns(6, 9);
+    assertFalse(cs.equals(cs2));
+    assertFalse(cs2.equals(cs));
+
     cs2.hideColumns(5, 8);
 
     assertTrue(cs.equals(cs2));
     assertTrue(cs.equals(cs));
     assertTrue(cs2.equals(cs));
     assertTrue(cs2.equals(cs2));
+
+    // different ranges, same size
+    cs.hideColumns(10, 12);
+    cs2.hideColumns(10, 15);
+    assertFalse(cs.equals(cs2));
+
   }
 
   @Test(groups = "Functional")
@@ -232,102 +215,50 @@ public class HiddenColumnsTest
     HiddenColumns cs = new HiddenColumns();
     cs.hideColumns(10, 11);
     cs.hideColumns(5, 7);
+    Iterator<int[]> regions = cs.iterator();
     assertEquals("[5, 7]",
-            Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
+            Arrays.toString(regions.next()));
 
     HiddenColumns cs2 = new HiddenColumns(cs);
+    regions = cs2.iterator();
     assertTrue(cs2.hasHiddenColumns());
-    assertEquals(2, cs2.getHiddenColumnsCopy().size());
+    assertEquals(2, cs2.getNumberOfRegions());
     // hidden columns are held in column order
     assertEquals("[5, 7]",
-            Arrays.toString(cs2.getHiddenColumnsCopy().get(0)));
+            Arrays.toString(regions.next()));
     assertEquals("[10, 11]",
-            Arrays.toString(cs2.getHiddenColumnsCopy().get(1)));
+            Arrays.toString(regions.next()));
   }
 
-  /**
-   * Test the code used to locate the reference sequence ruler origin
-   */
-  @Test(groups = { "Functional" })
-  public void testLocateVisibleBoundsofSequence()
+  @Test(groups = "Functional")
+  public void testCopyConstructor2()
   {
-    // create random alignment
-    AlignmentGenerator gen = new AlignmentGenerator(false);
-    AlignmentI al = gen.generate(50, 20, 123, 5, 5);
+    HiddenColumns cs = new HiddenColumns();
+    cs.hideColumns(10, 11);
+    cs.hideColumns(5, 7);
 
-    HiddenColumns cs = al.getHiddenColumns();
-    ColumnSelection colsel = new ColumnSelection();
+    HiddenColumns cs2 = new HiddenColumns(cs, 3, 9, 1);
+    assertTrue(cs2.hasHiddenColumns());
+    Iterator<int[]> regions = cs2.iterator();
 
-    SequenceI seq = new Sequence("RefSeq", "-A-SD-ASD--E---");
-    assertEquals(2, seq.findIndex(seq.getStart()));
-
-    // no hidden columns
-    assertEquals(
-            Arrays.toString(new int[] { seq.findIndex(seq.getStart()) - 1,
-                seq.findIndex(seq.getEnd()) - 1, seq.getStart(),
-                seq.getEnd(), seq.findIndex(seq.getStart()) - 1,
-                seq.findIndex(seq.getEnd()) - 1 }),
-            Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
-
-    // hidden column on gap after end of sequence - should not affect bounds
-    colsel.hideSelectedColumns(13, al.getHiddenColumns());
-    assertEquals(
-            Arrays.toString(new int[] { seq.findIndex(seq.getStart()) - 1,
-                seq.findIndex(seq.getEnd()) - 1, seq.getStart(),
-                seq.getEnd(), seq.findIndex(seq.getStart()) - 1,
-                seq.findIndex(seq.getEnd()) - 1 }),
-            Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
+    // only [5,7] returned, offset by 1
+    assertEquals("[4, 6]",
+            Arrays.toString(regions.next()));
+    assertEquals(3, cs2.getSize());
 
-    cs.revealAllHiddenColumns(colsel);
-    // hidden column on gap before beginning of sequence - should vis bounds by
-    // one
-    colsel.hideSelectedColumns(0, al.getHiddenColumns());
-    assertEquals(
-            Arrays.toString(new int[] { seq.findIndex(seq.getStart()) - 2,
-                seq.findIndex(seq.getEnd()) - 2, seq.getStart(),
-                seq.getEnd(), seq.findIndex(seq.getStart()) - 1,
-                seq.findIndex(seq.getEnd()) - 1 }),
-            Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
-
-    cs.revealAllHiddenColumns(colsel);
-    // hide columns around most of sequence - leave one residue remaining
-    cs.hideColumns(1, 3);
-    cs.hideColumns(6, 11);
-    assertEquals("-D",
-            cs.getVisibleSequenceStrings(0, 5, new SequenceI[] { seq })[0]);
-    assertEquals(
-            Arrays.toString(new int[] { 1, 1, 3, 3,
-                seq.findIndex(seq.getStart()) - 1,
-                seq.findIndex(seq.getEnd()) - 1 }),
-            Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
-    cs.revealAllHiddenColumns(colsel);
+    cs2 = new HiddenColumns(cs, 8, 15, 4);
+    regions = cs2.iterator();
+    assertTrue(cs2.hasHiddenColumns());
 
-    // hide whole sequence - should just get location of hidden region
-    // containing sequence
-    cs.hideColumns(1, 11);
-    assertEquals(
-            Arrays.toString(new int[] { 0, 1, 0, 0,
-                seq.findIndex(seq.getStart()) - 1,
-                seq.findIndex(seq.getEnd()) - 1 }),
-            Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
+    // only [10,11] returned, offset by 4
+    assertEquals("[6, 7]",
+            Arrays.toString(regions.next()));
+    assertEquals(2, cs2.getSize());
 
+    cs2 = new HiddenColumns(cs, 6, 10, 4);
+    assertFalse(cs2.hasHiddenColumns());
   }
 
-  @Test(groups = { "Functional" })
-  public void testLocateVisibleBoundsPathologicals()
-  {
-    // test some pathological cases we missed
-    AlignmentI al = new Alignment(new SequenceI[] { new Sequence(
-            "refseqGaptest", "KTDVTI----------NFI-----G----L") });
-    HiddenColumns cs = new HiddenColumns();
-    cs.hideInsertionsFor(al.getSequenceAt(0));
-    assertEquals(
-            "G",
-            ""
-                    + al.getSequenceAt(0).getCharAt(
-                            cs.adjustForHiddenColumns(9)));
-
-  }
 
   @Test(groups = { "Functional" })
   public void testHideColumns()
@@ -339,80 +270,103 @@ public class HiddenColumnsTest
     ColumnSelection colsel = new ColumnSelection();
     HiddenColumns cs = al.getHiddenColumns();
     colsel.hideSelectedColumns(5, al.getHiddenColumns());
-    List<int[]> hidden = cs.getHiddenColumnsCopy();
-    assertEquals(1, hidden.size());
-    assertEquals("[5, 5]", Arrays.toString(hidden.get(0)));
+    Iterator<int[]> regions = cs.iterator();
+    assertEquals(1, cs.getNumberOfRegions());
+    assertEquals("[5, 5]", Arrays.toString(regions.next()));
+    assertEquals(cs.getSize(), 1);
 
     colsel.hideSelectedColumns(3, al.getHiddenColumns());
-    hidden = cs.getHiddenColumnsCopy();
-    assertEquals(2, hidden.size());
+    regions = cs.iterator();
+    assertEquals(2, cs.getNumberOfRegions());
     // two hidden ranges, in order:
-    assertEquals(hidden.size(), cs.getHiddenColumnsCopy().size());
-    assertEquals("[3, 3]", Arrays.toString(hidden.get(0)));
-    assertEquals("[5, 5]", Arrays.toString(hidden.get(1)));
+    assertEquals("[3, 3]", Arrays.toString(regions.next()));
+    assertEquals("[5, 5]", Arrays.toString(regions.next()));
+    assertEquals(cs.getSize(), 2);
 
     // hiding column 4 expands [3, 3] to [3, 4]
     // and merges to [5, 5] to make [3, 5]
     colsel.hideSelectedColumns(4, al.getHiddenColumns());
-    hidden = cs.getHiddenColumnsCopy();
-    assertEquals(1, hidden.size());
-    assertEquals("[3, 5]", Arrays.toString(hidden.get(0)));
+    regions = cs.iterator();
+    assertEquals(1, cs.getNumberOfRegions());
+    assertEquals("[3, 5]", Arrays.toString(regions.next()));
+    assertEquals(cs.getSize(), 3);
 
     // clear hidden columns (note they are added to selected)
     cs.revealAllHiddenColumns(colsel);
     // it is now actually null but getter returns an empty list
-    assertTrue(cs.getHiddenColumnsCopy().isEmpty());
+    assertEquals(0, cs.getNumberOfRegions());
+    assertEquals(cs.getSize(), 0);
 
     cs.hideColumns(3, 6);
-    hidden = cs.getHiddenColumnsCopy();
-    int[] firstHiddenRange = hidden.get(0);
+    regions = cs.iterator();
+    int[] firstHiddenRange = regions.next();
     assertEquals("[3, 6]", Arrays.toString(firstHiddenRange));
+    assertEquals(cs.getSize(), 4);
 
     // adding a subrange of already hidden should do nothing
     cs.hideColumns(4, 5);
-    hidden = cs.getHiddenColumnsCopy();
-    assertEquals(1, hidden.size());
+    regions = cs.iterator();
+    assertEquals(1, cs.getNumberOfRegions());
     assertEquals("[3, 6]",
-            Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
+            Arrays.toString(regions.next()));
+    assertEquals(cs.getSize(), 4);
     cs.hideColumns(3, 5);
-    hidden = cs.getHiddenColumnsCopy();
-    assertEquals(1, hidden.size());
+    regions = cs.iterator();
+    assertEquals(1, cs.getNumberOfRegions());
     assertEquals("[3, 6]",
-            Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
+            Arrays.toString(regions.next()));
+    assertEquals(cs.getSize(), 4);
     cs.hideColumns(4, 6);
-    hidden = cs.getHiddenColumnsCopy();
-    assertEquals(1, hidden.size());
+    regions = cs.iterator();
+    assertEquals(1, cs.getNumberOfRegions());
     assertEquals("[3, 6]",
-            Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
+            Arrays.toString(regions.next()));
+    assertEquals(cs.getSize(), 4);
     cs.hideColumns(3, 6);
-    hidden = cs.getHiddenColumnsCopy();
-    assertEquals(1, hidden.size());
+    regions = cs.iterator();
+    assertEquals(1, cs.getNumberOfRegions());
     assertEquals("[3, 6]",
-            Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
+            Arrays.toString(regions.next()));
+    assertEquals(cs.getSize(), 4);
 
     cs.revealAllHiddenColumns(colsel);
     cs.hideColumns(2, 4);
-    hidden = cs.getHiddenColumnsCopy();
-    assertEquals(1, hidden.size());
-    assertEquals("[2, 4]", Arrays.toString(hidden.get(0)));
+    regions = cs.iterator();
+    assertEquals(1, cs.getNumberOfRegions());
+    assertEquals("[2, 4]", Arrays.toString(regions.next()));
+    assertEquals(cs.getSize(), 3);
 
     // extend contiguous with 2 positions overlap
     cs.hideColumns(3, 5);
-    hidden = cs.getHiddenColumnsCopy();
-    assertEquals(1, hidden.size());
-    assertEquals("[2, 5]", Arrays.toString(hidden.get(0)));
+    regions = cs.iterator();
+    assertEquals(1, cs.getNumberOfRegions());
+    assertEquals("[2, 5]", Arrays.toString(regions.next()));
+    assertEquals(cs.getSize(), 4);
 
     // extend contiguous with 1 position overlap
     cs.hideColumns(5, 6);
-    hidden = cs.getHiddenColumnsCopy();
-    assertEquals(1, hidden.size());
-    assertEquals("[2, 6]", Arrays.toString(hidden.get(0)));
+    regions = cs.iterator();
+    assertEquals(1, cs.getNumberOfRegions());
+    assertEquals("[2, 6]", Arrays.toString(regions.next()));
+    assertEquals(cs.getSize(), 5);
 
     // extend contiguous with overlap both ends:
     cs.hideColumns(1, 7);
-    hidden = cs.getHiddenColumnsCopy();
-    assertEquals(1, hidden.size());
-    assertEquals("[1, 7]", Arrays.toString(hidden.get(0)));
+    regions = cs.iterator();
+    assertEquals(1, cs.getNumberOfRegions());
+    assertEquals("[1, 7]", Arrays.toString(regions.next()));
+    assertEquals(cs.getSize(), 7);
+
+    cs.revealAllHiddenColumns(colsel);
+    cs.hideColumns(15, 18);
+    cs.hideColumns(2, 4);
+    cs.hideColumns(7, 9);
+    regions = cs.iterator();
+    assertEquals(3, cs.getNumberOfRegions());
+    assertEquals("[2, 4]", Arrays.toString(regions.next()));
+    assertEquals("[7, 9]", Arrays.toString(regions.next()));
+    assertEquals("[15, 18]", Arrays.toString(regions.next()));
+    assertEquals(cs.getSize(), 10);
   }
 
   /**
@@ -424,11 +378,18 @@ public class HiddenColumnsTest
   {
     ColumnSelection colsel = new ColumnSelection();
     HiddenColumns cs = new HiddenColumns();
+
+    // test with null hidden columns
+    cs.revealHiddenColumns(5, colsel);
+    assertTrue(colsel.getSelected().isEmpty());
+
     cs.hideColumns(5, 8);
     colsel.addElement(10);
     cs.revealHiddenColumns(5, colsel);
-    // hidden columns list now null but getter returns empty list:
-    assertTrue(cs.getHiddenColumnsCopy().isEmpty());
+
+    // hiddenColumns now empty
+    assertEquals(0, cs.getSize());
+
     // revealed columns are marked as selected (added to selection):
     assertEquals("[10, 5, 6, 7, 8]", colsel.getSelected().toString());
 
@@ -436,36 +397,67 @@ public class HiddenColumnsTest
     colsel = new ColumnSelection();
     cs = new HiddenColumns();
     cs.hideColumns(5, 8);
-    List<int[]> hidden = cs.getHiddenColumnsCopy();
+
+    int prevSize = cs.getSize();
     cs.revealHiddenColumns(6, colsel);
-    assertEquals(hidden.size(), cs.getHiddenColumnsCopy().size());
+    assertEquals(prevSize, cs.getSize());
+    assertTrue(colsel.getSelected().isEmpty());
+
+    // reveal hidden columns when there is more than one region
+    cs.hideColumns(20, 23);
+    // now there are 2 hidden regions
+    assertEquals(2, cs.getNumberOfRegions());
+
+    cs.revealHiddenColumns(20, colsel);
+
+    // hiddenColumns now has one region
+    assertEquals(1, cs.getNumberOfRegions());
+
+    // revealed columns are marked as selected (added to selection):
+    assertEquals("[20, 21, 22, 23]", colsel.getSelected().toString());
+
+    // call with a column past the end of the hidden column ranges
+    colsel.clear();
+    cs.revealHiddenColumns(20, colsel);
+    // hiddenColumns still has 1 region
+    assertEquals(1, cs.getNumberOfRegions());
     assertTrue(colsel.getSelected().isEmpty());
   }
 
   @Test(groups = { "Functional" })
   public void testRevealAllHiddenColumns()
   {
-    HiddenColumns cs = new HiddenColumns();
+    HiddenColumns hidden = new HiddenColumns();
     ColumnSelection colsel = new ColumnSelection();
-    cs.hideColumns(5, 8);
-    cs.hideColumns(2, 3);
+
+    // test with null hidden columns
+    hidden.revealAllHiddenColumns(colsel);
+    assertTrue(colsel.getSelected().isEmpty());
+
+    hidden.hideColumns(5, 8);
+    hidden.hideColumns(2, 3);
     colsel.addElement(11);
     colsel.addElement(1);
-    cs.revealAllHiddenColumns(colsel);
+    hidden.revealAllHiddenColumns(colsel);
 
     /*
      * revealing hidden columns adds them (in order) to the (unordered)
      * selection list
      */
-    assertTrue(cs.getHiddenColumnsCopy().isEmpty());
-    assertEquals("[11, 1, 2, 3, 5, 6, 7, 8]", colsel.getSelected()
-            .toString());
+
+    // hiddenColumns now empty
+    assertEquals(0, hidden.getSize());
+
+    assertEquals("[11, 1, 2, 3, 5, 6, 7, 8]",
+            colsel.getSelected().toString());
   }
 
   @Test(groups = { "Functional" })
   public void testIsVisible()
   {
     HiddenColumns cs = new HiddenColumns();
+    assertTrue(cs.isVisible(5));
+
     cs.hideColumns(2, 4);
     cs.hideColumns(6, 7);
     assertTrue(cs.isVisible(0));
@@ -477,6 +469,7 @@ public class HiddenColumnsTest
     assertTrue(cs.isVisible(5));
     assertFalse(cs.isVisible(6));
     assertFalse(cs.isVisible(7));
+    assertTrue(cs.isVisible(8));
   }
 
   /**
@@ -493,15 +486,17 @@ public class HiddenColumnsTest
     HiddenColumns cs = new HiddenColumns();
     cs.hideColumns(49, 59);
     cs.hideColumns(69, 79);
-    List<int[]> hidden = cs.getHiddenColumnsCopy();
-    assertEquals(2, hidden.size());
-    assertEquals("[49, 59]", Arrays.toString(hidden.get(0)));
-    assertEquals("[69, 79]", Arrays.toString(hidden.get(1)));
+    Iterator<int[]> regions = cs.iterator();
+    assertEquals(2, cs.getNumberOfRegions());
+    assertEquals("[49, 59]", Arrays.toString(regions.next()));
+    assertEquals("[69, 79]", Arrays.toString(regions.next()));
+    assertEquals(22, cs.getSize());
 
     cs.hideColumns(48, 80);
-    hidden = cs.getHiddenColumnsCopy();
-    assertEquals(1, hidden.size());
-    assertEquals("[48, 80]", Arrays.toString(hidden.get(0)));
+    regions = cs.iterator();
+    assertEquals(1, cs.getNumberOfRegions());
+    assertEquals("[48, 80]", Arrays.toString(regions.next()));
+    assertEquals(33, cs.getSize());
 
     /*
      * another...joining hidden ranges
@@ -512,9 +507,10 @@ public class HiddenColumnsTest
     cs.hideColumns(50, 60);
     // hiding 21-49 should merge to one range
     cs.hideColumns(21, 49);
-    hidden = cs.getHiddenColumnsCopy();
-    assertEquals(1, hidden.size());
-    assertEquals("[10, 60]", Arrays.toString(hidden.get(0)));
+    regions = cs.iterator();
+    assertEquals(1, cs.getNumberOfRegions());
+    assertEquals("[10, 60]", Arrays.toString(regions.next()));
+    assertEquals(51, cs.getSize());
 
     /*
      * another...left overlap, subsumption, right overlap,
@@ -528,14 +524,15 @@ public class HiddenColumnsTest
     cs.hideColumns(60, 70);
 
     cs.hideColumns(15, 45);
-    hidden = cs.getHiddenColumnsCopy();
-    assertEquals(2, hidden.size());
-    assertEquals("[10, 50]", Arrays.toString(hidden.get(0)));
-    assertEquals("[60, 70]", Arrays.toString(hidden.get(1)));
+    regions = cs.iterator();
+    assertEquals(2, cs.getNumberOfRegions());
+    assertEquals("[10, 50]", Arrays.toString(regions.next()));
+    assertEquals("[60, 70]", Arrays.toString(regions.next()));
+    assertEquals(52, cs.getSize());
   }
 
   @Test(groups = { "Functional" })
-  public void testHideBitset()
+  public void testHideColumns_BitSet()
   {
     HiddenColumns cs;
 
@@ -544,80 +541,45 @@ public class HiddenColumnsTest
     // one hidden range
     one.set(1);
     cs = new HiddenColumns();
-    cs.hideMarkedBits(one);
-    assertEquals(1, cs.getHiddenColumnsCopy().size());
+    cs.hideColumns(one);
+    assertEquals(1, cs.getNumberOfRegions());
+    assertEquals(1, cs.getSize());
 
     one.set(2);
     cs = new HiddenColumns();
-    cs.hideMarkedBits(one);
-    assertEquals(1, cs.getHiddenColumnsCopy().size());
+    cs.hideColumns(one);
+    assertEquals(1, cs.getNumberOfRegions());
+    assertEquals(2, cs.getSize());
 
     one.set(3);
     cs = new HiddenColumns();
-    cs.hideMarkedBits(one);
-    assertEquals(1, cs.getHiddenColumnsCopy().size());
+    cs.hideColumns(one);
+    assertEquals(1, cs.getNumberOfRegions());
+    assertEquals(3, cs.getSize());
 
     // split
     one.clear(2);
     cs = new HiddenColumns();
-    cs.hideMarkedBits(one);
-    assertEquals(2, cs.getHiddenColumnsCopy().size());
+    cs.hideColumns(one);
+    assertEquals(2, cs.getNumberOfRegions());
+    assertEquals(2, cs.getSize());
 
-    assertEquals(0, cs.adjustForHiddenColumns(0));
-    assertEquals(2, cs.adjustForHiddenColumns(1));
-    assertEquals(4, cs.adjustForHiddenColumns(2));
+    assertEquals(0, cs.visibleToAbsoluteColumn(0));
+    assertEquals(2, cs.visibleToAbsoluteColumn(1));
+    assertEquals(4, cs.visibleToAbsoluteColumn(2));
 
     // one again
     one.clear(1);
     cs = new HiddenColumns();
-    cs.hideMarkedBits(one);
+    cs.hideColumns(one);
+    assertEquals(1, cs.getSize());
 
-    assertEquals(1, cs.getHiddenColumnsCopy().size());
+    assertEquals(1, cs.getNumberOfRegions());
 
-    assertEquals(0, cs.adjustForHiddenColumns(0));
-    assertEquals(1, cs.adjustForHiddenColumns(1));
-    assertEquals(2, cs.adjustForHiddenColumns(2));
-    assertEquals(4, cs.adjustForHiddenColumns(3));
-  }
-
-  @Test(groups = { "Functional" })
-  public void testGetBitset()
-  {
-    BitSet toMark, fromMark;
-    long seed = -3241532;
-    Random number = new Random(seed);
-    for (int n = 0; n < 1000; n++)
-    {
-      // create a random bitfield
-      toMark = BitSet.valueOf(new long[] { number.nextLong(),
-          number.nextLong(), number.nextLong() });
-      toMark.set(n * number.nextInt(10), n * (25 + number.nextInt(25)));
-      HiddenColumns hc = new HiddenColumns();
-      hc.hideMarkedBits(toMark);
-
-      // see if we can recover bitfield
-      hc.markHiddenRegions(fromMark = new BitSet());
-      assertEquals(toMark, fromMark);
-    }
-  }
-
-  @Test(groups = { "Functional" })
-  public void testFindHiddenRegionPositions()
-  {
-    HiddenColumns hc = new HiddenColumns();
-
-    List<Integer> positions = hc.findHiddenRegionPositions();
-    assertTrue(positions.isEmpty());
-
-    hc.hideColumns(3, 7);
-    hc.hideColumns(10, 10);
-    hc.hideColumns(14, 15);
-
-    positions = hc.findHiddenRegionPositions();
-    assertEquals(3, positions.size());
-    assertEquals(3, positions.get(0).intValue());
-    assertEquals(5, positions.get(1).intValue());
-    assertEquals(8, positions.get(2).intValue());
+    assertEquals(0, cs.visibleToAbsoluteColumn(0));
+    assertEquals(1, cs.visibleToAbsoluteColumn(1));
+    assertEquals(2, cs.visibleToAbsoluteColumn(2));
+    assertEquals(4, cs.visibleToAbsoluteColumn(3));
   }
 
   @Test(groups = { "Functional" })
@@ -637,7 +599,7 @@ public class HiddenColumnsTest
   }
 
   @Test(groups = "Functional")
-  public void getVisibleStartAndEndIndexTest()
+  public void testGetVisibleStartAndEndIndex()
   {
     Sequence seq = new Sequence("testSeq", "ABCDEFGHIJKLMNOPQRSTUVWXYZ");
     AlignmentI align = new Alignment(new SequenceI[] { seq });
@@ -663,6 +625,13 @@ public class HiddenColumnsTest
     System.out.println(startEnd[0] + " : " + startEnd[1]);
     assertEquals(1, startEnd[0]);
     assertEquals(23, startEnd[1]);
+
+    // force lowest range to start of alignment
+    hc = new HiddenColumns();
+    hc.hideColumns(3, 4);
+    startEnd = hc.getVisibleStartAndEndIndex(align.getWidth());
+    assertEquals(0, startEnd[0]);
+    assertEquals(25, startEnd[1]);
   }
 
   @Test(groups = "Functional")
@@ -677,58 +646,683 @@ public class HiddenColumnsTest
     hc.hideColumns(10, 10);
     hc.hideColumns(14, 15);
 
-    result = hc.getRegionWithEdgeAtRes(3);
+    result = hc.getRegionWithEdgeAtRes(2);
     assertEquals(3, result[0]);
     assertEquals(7, result[1]);
 
+    result = hc.getRegionWithEdgeAtRes(4);
+    assertEquals(10, result[0]);
+    assertEquals(10, result[1]);
+
     result = hc.getRegionWithEdgeAtRes(5);
     assertEquals(10, result[0]);
     assertEquals(10, result[1]);
 
     result = hc.getRegionWithEdgeAtRes(6);
     assertNull(result);
+
+    result = hc.getRegionWithEdgeAtRes(0);
+    assertNull(result);
+
+    result = hc.getRegionWithEdgeAtRes(7);
+    assertEquals(14, result[0]);
+    assertEquals(15, result[1]);
+
+    result = hc.getRegionWithEdgeAtRes(8);
+    assertEquals(14, result[0]);
+    assertEquals(15, result[1]);
+
+    result = hc.getRegionWithEdgeAtRes(16);
+    assertNull(result);
   }
 
   @Test(groups = "Functional")
-  public void testPropagateInsertions()
+  public void testHasHiddenColumns()
   {
-    // create an alignment with no gaps - this will be the profile seq and other
-    // JPRED seqs
-    AlignmentGenerator gen = new AlignmentGenerator(false);
-    AlignmentI al = gen.generate(20, 10, 1234, 0, 0);
-
-    // get the profileseq
-    SequenceI profileseq = al.getSequenceAt(0);
-    SequenceI gappedseq = new Sequence(profileseq);
-    gappedseq.insertCharAt(5, al.getGapCharacter());
-    gappedseq.insertCharAt(6, al.getGapCharacter());
-    gappedseq.insertCharAt(7, al.getGapCharacter());
-    gappedseq.insertCharAt(8, al.getGapCharacter());
-    
-    // create an alignment view with the gapped sequence
-    SequenceI[] seqs = new SequenceI[1];
-    seqs[0] = gappedseq;
-    AlignmentI newal = new Alignment(seqs);
-    HiddenColumns hidden = new HiddenColumns();
-    hidden.hideColumns(15, 17);
-
-    AlignmentView view = new AlignmentView(newal, hidden, null, true, false,
-            false);
-
-    // confirm that original contigs are as expected
-    int[] oldcontigs = hidden.getVisibleContigs(0, 20);
-    int[] testcontigs = { 0, 14, 18, 19 };
-    assertTrue(Arrays.equals(oldcontigs, testcontigs));
-            
-    // propagate insertions
-    HiddenColumns result = HiddenColumns.propagateInsertions(profileseq, al,
-            view);
-
-    // confirm that the contigs have changed to account for the gaps
-    int[] newcontigs = result.getVisibleContigs(0, 20);
-    testcontigs[1] = 10;
-    testcontigs[2] = 14;
-    assertTrue(Arrays.equals(newcontigs, testcontigs));
-    
+    HiddenColumns h = new HiddenColumns();
+
+    // new HiddenColumns2 has no hidden cols
+    assertFalse(h.hasHiddenColumns());
+
+    // some columns hidden, returns true
+    h.hideColumns(5, 10);
+    assertTrue(h.hasHiddenColumns());
+
+    // reveal columns, no hidden cols again
+    ColumnSelection sel = new ColumnSelection();
+    h.revealAllHiddenColumns(sel);
+    assertFalse(h.hasHiddenColumns());
+  }
+
+  @Test(groups = "Functional")
+  public void testHasManyHiddenColumns()
+  {
+    HiddenColumns h = new HiddenColumns();
+
+    // h has no hidden cols
+    assertFalse(h.hasMultiHiddenColumnRegions());
+
+    // one set of columns hidden, returns false
+    h.hideColumns(5, 10);
+    assertFalse(h.hasMultiHiddenColumnRegions());
+
+    // two sets hidden, returns true
+    h.hideColumns(15, 17);
+    assertTrue(h.hasMultiHiddenColumnRegions());
+
+    // back to one block, asserts false
+    h.hideColumns(11, 14);
+    assertFalse(h.hasMultiHiddenColumnRegions());
+  }
+
+  @Test(groups = "Functional")
+  public void testAdjustForHiddenColumns()
+  {
+    HiddenColumns h = new HiddenColumns();
+    // returns input value when there are no hidden columns
+    assertEquals(10, h.visibleToAbsoluteColumn(10));
+
+    h.hideColumns(20, 30);
+    assertEquals(10, h.visibleToAbsoluteColumn(10));
+    assertEquals(20 + 11, h.visibleToAbsoluteColumn(20));
+    assertEquals(35 + 11, h.visibleToAbsoluteColumn(35));
+
+    h.hideColumns(5, 7);
+    assertEquals(10 + 3, h.visibleToAbsoluteColumn(10));
+    assertEquals(20 + 14, h.visibleToAbsoluteColumn(20));
+    assertEquals(35 + 14, h.visibleToAbsoluteColumn(35));
+
+    ColumnSelection sel = new ColumnSelection();
+    h.revealAllHiddenColumns(sel);
+    h.hideColumns(0, 1);
+    assertEquals(4, h.visibleToAbsoluteColumn(2));
+  }
+
+  @Test(groups = "Functional")
+  public void testGetNextHiddenBoundary_Left()
+  {
+    HiddenColumns h = new HiddenColumns();
+
+    // returns same value if no hidden cols
+    assertEquals(3, h.getNextHiddenBoundary(true, 3));
+
+    h.hideColumns(5, 10);
+    assertEquals(10, h.getNextHiddenBoundary(true, 15));
+    assertEquals(3, h.getNextHiddenBoundary(true, 3));
+    assertEquals(7, h.getNextHiddenBoundary(true, 7));
+
+    h.hideColumns(15, 20);
+    assertEquals(10, h.getNextHiddenBoundary(true, 15));
+    assertEquals(20, h.getNextHiddenBoundary(true, 21));
+  }
+
+  @Test(groups = "Functional")
+  public void testGetNextHiddenBoundary_Right()
+  {
+    HiddenColumns h = new HiddenColumns();
+
+    // returns same value if no hidden cols
+    assertEquals(3, h.getNextHiddenBoundary(false, 3));
+
+    h.hideColumns(5, 10);
+    assertEquals(5, h.getNextHiddenBoundary(false, 3));
+    assertEquals(15, h.getNextHiddenBoundary(false, 15));
+    assertEquals(7, h.getNextHiddenBoundary(false, 7));
+
+    h.hideColumns(15, 20);
+    assertEquals(15, h.getNextHiddenBoundary(false, 7));
+    assertEquals(15, h.getNextHiddenBoundary(false, 14));
+
+    // returns same value if there is no next hidden column
+    assertEquals(22, h.getNextHiddenBoundary(false, 22));
+  }
+
+  @Test(groups = "Functional")
+  public void testIterator()
+  {
+    HiddenColumns h = new HiddenColumns();
+    Iterator<int[]> result = h.iterator();
+    assertFalse(result.hasNext());
+
+    h.hideColumns(5, 10);
+    result = h.iterator();
+    int[] next = result.next();
+    assertEquals(5, next[0]);
+    assertEquals(10, next[1]);
+    assertFalse(result.hasNext());
+
+    h.hideColumns(22, 23);
+    result = h.iterator();
+    next = result.next();
+    assertEquals(5, next[0]);
+    assertEquals(10, next[1]);
+    next = result.next();
+    assertEquals(22, next[0]);
+    assertEquals(23, next[1]);
+    assertFalse(result.hasNext());
+
+    // test for only one hidden region at start of alignment
+    ColumnSelection sel = new ColumnSelection();
+    h.revealAllHiddenColumns(sel);
+    h.hideColumns(0, 1);
+    result = h.iterator();
+    next = result.next();
+    assertEquals(0, next[0]);
+    assertEquals(1, next[1]);
+    assertFalse(result.hasNext());
+  }
+
+  /* @Test(groups = "Functional")
+  public void testGetVisibleSequenceStrings()
+  {
+    HiddenColumns h = new HiddenColumns();
+    SequenceI seq1 = new Sequence("TEST1", "GALMFWKQESPVICYHRNDT");
+    SequenceI seq2 = new Sequence("TEST2", "VICYHRNDTGA");
+    SequenceI[] seqs = new SequenceI[2];
+    seqs[0] = seq1;
+    seqs[1] = seq2;
+    String[] result = h.getVisibleSequenceStrings(5, 10, seqs);
+    assertEquals(2, result.length);
+    assertEquals("WKQES", result[0]);
+    assertEquals("RNDTG", result[1]);
+  
+    h.hideColumns(6, 8);
+    result = h.getVisibleSequenceStrings(5, 10, seqs);
+    assertEquals(2, result.length);
+    assertEquals("WS", result[0]);
+    assertEquals("RG", result[1]);
+  
+    SequenceI seq = new Sequence("RefSeq", "-A-SD-ASD--E---");
+    ColumnSelection sel = new ColumnSelection();
+    h.revealAllHiddenColumns(sel);
+    h.hideColumns(1, 3);
+    h.hideColumns(6, 11);
+    assertEquals("-D",
+            h.getVisibleSequenceStrings(0, 5, new SequenceI[]
+    { seq })[0]);
+  }*/
+
+  @Test(groups = "Functional")
+  public void testHideInsertionsFor()
+  {
+    HiddenColumns h = new HiddenColumns();
+    HiddenColumns h2 = new HiddenColumns();
+    SequenceI seq1 = new Sequence("TEST1", "GAL---MFW-KQESPVICY--HRNDT");
+    SequenceI seq2 = new Sequence("TEST1", "GALMFWKQESPVICYHRNDT");
+
+    h.hideList(seq2.getInsertions());
+    assertTrue(h.equals(h2));
+    assertEquals(0, h.getSize());
+
+    h.hideList(seq1.getInsertions());
+    h2.hideColumns(3, 5);
+    h2.hideColumns(9, 9);
+    h2.hideColumns(19, 20);
+    assertTrue(h.equals(h2));
+    assertEquals(6, h.getSize());
+  }
+
+  @Test(groups = "Functional")
+  public void testHideColumns_BitSet_range()
+  {
+    HiddenColumns h = new HiddenColumns();
+    HiddenColumns h2 = new HiddenColumns();
+
+    BitSet tohide = new BitSet(25);
+    h.hideColumns(tohide);
+    assertTrue(h.equals(h2));
+
+    // when setting bitset, first param is inclusive, second exclusive
+    tohide.set(3, 6);
+    tohide.set(9);
+    tohide.set(15, 21);
+    h.clearAndHideColumns(tohide, 5, 23);
+
+    h2.hideColumns(5, 5);
+    h2.hideColumns(9, 9);
+    h2.hideColumns(15, 20);
+    assertTrue(h.equals(h2));
+    assertEquals(h.getSize(), h2.getSize());
+
+    tohide.clear();
+    tohide.set(41);
+    h.clearAndHideColumns(tohide, 23, 30);
+    assertTrue(h.equals(h2));
+    assertEquals(h.getSize(), h2.getSize());
+
+    tohide.set(41);
+    h.clearAndHideColumns(tohide, 30, 45);
+    h2.hideColumns(41, 41);
+    assertTrue(h.equals(h2));
+    assertEquals(h.getSize(), h2.getSize());
+
+    tohide.clear();
+    tohide.set(25, 28);
+    h.clearAndHideColumns(tohide, 17, 50);
+    h2 = new HiddenColumns();
+    h2.hideColumns(5, 5);
+    h2.hideColumns(9, 9);
+    h2.hideColumns(15, 16);
+    h2.hideColumns(25, 27);
+    assertTrue(h.equals(h2));
+    assertEquals(h.getSize(), h2.getSize());
+
+    HiddenColumns hc = new HiddenColumns();
+    hc.hideColumns(3, 5);
+    hc.hideColumns(15, 20);
+    hc.hideColumns(45, 60);
+
+    tohide = new BitSet();
+
+    // all unhidden if tohide is empty and range covers hidden
+    hc.clearAndHideColumns(tohide, 1, 70);
+    assertTrue(!hc.hasHiddenColumns());
+    assertEquals(0, hc.getSize());
+
+    hc.hideColumns(3, 5);
+    hc.hideColumns(15, 20);
+    hc.hideColumns(45, 60);
+    assertEquals(25, hc.getSize());
+
+    // but not if range does not cover hidden
+    hc.clearAndHideColumns(tohide, 23, 40);
+    assertTrue(hc.hasHiddenColumns());
+    assertEquals(25, hc.getSize());
+
+    // and partial unhide if range partially covers
+    hc.clearAndHideColumns(tohide, 1, 17);
+    Iterator<int[]> it = hc.iterator();
+    assertTrue(it.hasNext());
+    int[] region = it.next();
+
+    assertEquals(18, region[0]);
+    assertEquals(20, region[1]);
+
+    assertTrue(it.hasNext());
+    region = it.next();
+
+    assertEquals(45, region[0]);
+    assertEquals(60, region[1]);
+
+    assertFalse(it.hasNext());
+    assertEquals(19, hc.getSize());
+  }
+
+  @Test(groups = "Functional")
+  public void testOffsetByVisibleColumns()
+  {
+    HiddenColumns h = new HiddenColumns();
+    int result = h.offsetByVisibleColumns(-1, 10);
+    assertEquals(9, result);
+
+    h.hideColumns(7, 9);
+    result = h.offsetByVisibleColumns(-4, 10);
+    assertEquals(3, result);
+
+    h.hideColumns(14, 15);
+    result = h.offsetByVisibleColumns(-4, 10);
+    assertEquals(3, result);
+
+    result = h.offsetByVisibleColumns(-10, 17);
+    assertEquals(2, result);
+
+    result = h.offsetByVisibleColumns(-1, 7);
+    assertEquals(5, result);
+
+    result = h.offsetByVisibleColumns(-1, 8);
+    assertEquals(5, result);
+
+    result = h.offsetByVisibleColumns(-3, 15);
+    assertEquals(10, result);
+
+    ColumnSelection sel = new ColumnSelection();
+    h.revealAllHiddenColumns(sel);
+    h.hideColumns(0, 30);
+    result = h.offsetByVisibleColumns(-31, 0);
+    assertEquals(-31, result);
+
+    HiddenColumns cs = new HiddenColumns();
+
+    // test that without hidden columns, offsetByVisibleColumns returns
+    // position n to left of provided position
+    long pos = cs.offsetByVisibleColumns(-3, 10);
+    assertEquals(7, pos);
+
+    // 0 returns same position
+    pos = cs.offsetByVisibleColumns(0, 10);
+    assertEquals(10, pos);
+
+    // overflow to left returns negative number
+    pos = cs.offsetByVisibleColumns(-3, 0);
+    assertEquals(-3, pos);
+
+    // test that with hidden columns to left of result column
+    // behaviour is the same as above
+    cs.hideColumns(1, 3);
+
+    // position n to left of provided position
+    pos = cs.offsetByVisibleColumns(-3, 10);
+    assertEquals(7, pos);
+
+    // 0 returns same position
+    pos = cs.offsetByVisibleColumns(0, 10);
+    assertEquals(10, pos);
+
+    // test with one set of hidden columns between start and required position
+    cs.hideColumns(12, 15);
+    pos = cs.offsetByVisibleColumns(-8, 17);
+    assertEquals(5, pos);
+
+    // test with two sets of hidden columns between start and required position
+    cs.hideColumns(20, 21);
+    pos = cs.offsetByVisibleColumns(-8, 23);
+    assertEquals(9, pos);
+
+    // repeat last 2 tests with no hidden columns to left of required position
+    ColumnSelection colsel = new ColumnSelection();
+    cs.revealAllHiddenColumns(colsel);
+
+    // test with one set of hidden columns between start and required position
+    cs.hideColumns(12, 15);
+    pos = cs.offsetByVisibleColumns(-8, 17);
+    assertEquals(5, pos);
+
+    // test with two sets of hidden columns between start and required position
+    cs.hideColumns(20, 21);
+    pos = cs.offsetByVisibleColumns(-8, 23);
+    assertEquals(9, pos);
+
+    // test with right (positive) offsets
+
+    // test that without hidden columns, offsetByVisibleColumns returns
+    // position n to right of provided position
+    pos = cs.offsetByVisibleColumns(3, 7);
+    assertEquals(10, pos);
+
+    // test that with hidden columns to left of result column
+    // behaviour is the same as above
+    cs.hideColumns(1, 3);
+
+    // test with one set of hidden columns between start and required position
+    cs.hideColumns(12, 15);
+    pos = cs.offsetByVisibleColumns(8, 5);
+    assertEquals(17, pos);
+
+    // test with two sets of hidden columns between start and required position
+    cs.hideColumns(20, 21);
+    pos = cs.offsetByVisibleColumns(8, 9);
+    assertEquals(23, pos);
+
+    // repeat last 2 tests with no hidden columns to left of required position
+    colsel = new ColumnSelection();
+    cs.revealAllHiddenColumns(colsel);
+
+    // test with one set of hidden columns between start and required position
+    cs.hideColumns(12, 15);
+    pos = cs.offsetByVisibleColumns(8, 5);
+    assertEquals(17, pos);
+
+    // test with two sets of hidden columns between start and required position
+    cs.hideColumns(20, 21);
+    pos = cs.offsetByVisibleColumns(8, 9);
+    assertEquals(23, pos);
+  }
+
+  @Test(groups = "Functional")
+  public void testBoundedIterator()
+  {
+    HiddenColumns h = new HiddenColumns();
+    Iterator<int[]> it = h.getBoundedIterator(0, 10);
+
+    // no hidden columns = nothing to iterate over
+    assertFalse(it.hasNext());
+
+    // [start,end] contains all hidden columns
+    // all regions are returned
+    h.hideColumns(3, 10);
+    h.hideColumns(14, 16);
+    it = h.getBoundedIterator(0, 20);
+    assertTrue(it.hasNext());
+    int[] next = it.next();
+    assertEquals(3, next[0]);
+    assertEquals(10, next[1]);
+    next = it.next();
+    assertEquals(14, next[0]);
+    assertEquals(16, next[1]);
+    assertFalse(it.hasNext());
+
+    // [start,end] overlaps a region
+    // 1 region returned
+    it = h.getBoundedIterator(5, 7);
+    assertTrue(it.hasNext());
+    next = it.next();
+    assertEquals(3, next[0]);
+    assertEquals(10, next[1]);
+    assertFalse(it.hasNext());
+
+    // [start,end] fully contains 1 region and start of last
+    // - 2 regions returned
+    it = h.getBoundedIterator(3, 15);
+    assertTrue(it.hasNext());
+    next = it.next();
+    assertEquals(3, next[0]);
+    assertEquals(10, next[1]);
+    next = it.next();
+    assertEquals(14, next[0]);
+    assertEquals(16, next[1]);
+    assertFalse(it.hasNext());
+
+    // [start,end] contains end of first region and whole of last region
+    // - 2 regions returned
+    it = h.getBoundedIterator(4, 20);
+    assertTrue(it.hasNext());
+    next = it.next();
+    assertEquals(3, next[0]);
+    assertEquals(10, next[1]);
+    next = it.next();
+    assertEquals(14, next[0]);
+    assertEquals(16, next[1]);
+    assertFalse(it.hasNext());
+  }
+
+  @Test(groups = "Functional")
+  public void testBoundedStartIterator()
+  {
+    HiddenColumns h = new HiddenColumns();
+    Iterator<Integer> it = h.getStartRegionIterator(0, 10);
+
+    // no hidden columns = nothing to iterate over
+    assertFalse(it.hasNext());
+
+    // [start,end] contains all hidden columns
+    // all regions are returned
+    h.hideColumns(3, 10);
+    h.hideColumns(14, 16);
+    it = h.getStartRegionIterator(0, 20);
+    assertTrue(it.hasNext());
+    int next = it.next();
+    assertEquals(3, next);
+    next = it.next();
+    assertEquals(6, next);
+    assertFalse(it.hasNext());
+
+    // [start,end] does not contain a start of a region
+    // no regions to iterate over
+    it = h.getStartRegionIterator(4, 5);
+    assertFalse(it.hasNext());
+
+    // [start,end] fully contains 1 region and start of last
+    // - 2 regions returned
+    it = h.getStartRegionIterator(3, 7);
+    assertTrue(it.hasNext());
+    next = it.next();
+    assertEquals(3, next);
+    next = it.next();
+    assertEquals(6, next);
+    assertFalse(it.hasNext());
+
+    // [start,end] contains whole of last region
+    // - 1 region returned
+    it = h.getStartRegionIterator(4, 20);
+    assertTrue(it.hasNext());
+    next = it.next();
+    assertEquals(6, next);
+    assertFalse(it.hasNext());
+  }
+
+  @Test(groups = "Functional")
+  public void testVisibleBlocksVisBoundsIterator()
+  {
+    HiddenColumns h = new HiddenColumns();
+    Iterator<int[]> regions = h.getVisContigsIterator(0, 31, true);
+
+    // only 1 visible region spanning 0-30 if nothing is hidden
+    assertTrue(regions.hasNext());
+    int[] region = regions.next();
+    assertEquals(0, region[0]);
+    assertEquals(30, region[1]);
+    assertFalse(regions.hasNext());
+
+    // hide 1 region in middle
+    // 2 regions one on either side
+    // second region boundary accounts for hidden columns
+    h.hideColumns(10, 15);
+    regions = h.getVisContigsIterator(0, 31, true);
+
+    assertTrue(regions.hasNext());
+    region = regions.next();
+    assertEquals(0, region[0]);
+    assertEquals(9, region[1]);
+    region = regions.next();
+    assertEquals(16, region[0]);
+    assertEquals(36, region[1]);
+    assertFalse(regions.hasNext());
+
+    // single hidden region at left
+    h = new HiddenColumns();
+    h.hideColumns(0, 5);
+    regions = h.getVisContigsIterator(0, 31, true);
+
+    assertTrue(regions.hasNext());
+    region = regions.next();
+    assertEquals(6, region[0]);
+    assertEquals(36, region[1]);
+    assertFalse(regions.hasNext());
+
+    // single hidden region at right
+    h = new HiddenColumns();
+    h.hideColumns(27, 30);
+    regions = h.getVisContigsIterator(0, 31, true);
+
+    assertTrue(regions.hasNext());
+    region = regions.next();
+    assertEquals(0, region[0]);
+    assertEquals(26, region[1]);
+    region = regions.next();
+    assertEquals(31, region[0]);
+    assertEquals(34, region[1]);
+    assertFalse(regions.hasNext());
+
+    // hidden region at left + hidden region in middle
+    h = new HiddenColumns();
+    h.hideColumns(0, 5);
+    h.hideColumns(23, 25);
+    regions = h.getVisContigsIterator(0, 31, true);
+
+    assertTrue(regions.hasNext());
+    region = regions.next();
+    assertEquals(6, region[0]);
+    assertEquals(22, region[1]);
+    region = regions.next();
+    assertEquals(26, region[0]);
+    assertEquals(39, region[1]);
+    assertFalse(regions.hasNext());
+
+    // hidden region at right + hidden region in middle
+    h = new HiddenColumns();
+    h.hideColumns(27, 30);
+    h.hideColumns(11, 14);
+    regions = h.getVisContigsIterator(0, 31, true);
+
+    assertTrue(regions.hasNext());
+    region = regions.next();
+    assertEquals(0, region[0]);
+    assertEquals(10, region[1]);
+    region = regions.next();
+    assertEquals(15, region[0]);
+    assertEquals(26, region[1]);
+    region = regions.next();
+    assertEquals(31, region[0]);
+    assertEquals(38, region[1]);
+    assertFalse(regions.hasNext());
+
+    // hidden region at left and right
+    h = new HiddenColumns();
+    h.hideColumns(27, 35);
+    h.hideColumns(0, 4);
+    regions = h.getVisContigsIterator(0, 31, true);
+
+    assertTrue(regions.hasNext());
+    region = regions.next();
+    assertEquals(5, region[0]);
+    assertEquals(26, region[1]);
+    region = regions.next();
+    assertEquals(36, region[0]);
+    assertEquals(44, region[1]);
+    assertFalse(regions.hasNext());
+
+    // multiple hidden regions
+    h = new HiddenColumns();
+    h.hideColumns(1, 1);
+    h.hideColumns(3, 5);
+    h.hideColumns(9, 11);
+    h.hideColumns(22, 26);
+
+    regions = h.getVisContigsIterator(0, 31, true);
+
+    assertTrue(regions.hasNext());
+    region = regions.next();
+    assertEquals(0, region[0]);
+    assertEquals(0, region[1]);
+    region = regions.next();
+    assertEquals(2, region[0]);
+    assertEquals(2, region[1]);
+    region = regions.next();
+    assertEquals(6, region[0]);
+    assertEquals(8, region[1]);
+    region = regions.next();
+    assertEquals(12, region[0]);
+    assertEquals(21, region[1]);
+    region = regions.next();
+    assertEquals(27, region[0]);
+    assertEquals(42, region[1]);
+    assertFalse(regions.hasNext());
+  }
+
+  /*
+   * the VisibleColsIterator is tested elsewhere, this just tests that 
+   * it can be retrieved from HiddenColumns
+   */
+  @Test(groups = "Functional")
+  public void testGetVisibleColsIterator()
+  {
+    HiddenColumns h = new HiddenColumns();
+    Iterator<Integer> it = h.getVisibleColsIterator(0, 10);
+
+    assertTrue(it instanceof RangeElementsIterator);
+  }
+
+  @Test(groups = "Functional")
+  public void testHashCode()
+  {
+    HiddenColumns h = new HiddenColumns();
+    h.hideColumns(0, 25);
+
+    int result = h.hashCode();
+    assertTrue(result > 0);
+
+    h.hideColumns(30, 50);
+    assertTrue(h.hashCode() > 0);
+    assertTrue(result != h.hashCode());
   }
 }
diff --git a/test/jalview/datamodel/HiddenMarkovModelTest.java b/test/jalview/datamodel/HiddenMarkovModelTest.java
new file mode 100644
index 0000000..7978da2
--- /dev/null
+++ b/test/jalview/datamodel/HiddenMarkovModelTest.java
@@ -0,0 +1,146 @@
+package jalview.datamodel;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.io.DataSourceType;
+import jalview.io.FileParse;
+import jalview.io.HMMFile;
+import jalview.schemes.ResidueProperties;
+
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.util.Map;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+public class HiddenMarkovModelTest {
+
+  HiddenMarkovModel hmm;
+
+  @BeforeClass(alwaysRun = true)
+  public void setUp() throws MalformedURLException, IOException
+  {
+    /*
+     * load hmm model of a Kinase domain to a HiddenMarkovModel
+     */
+    HMMFile file = new HMMFile(new FileParse(
+            "test/jalview/io/test_PKinase_hmm.txt", DataSourceType.FILE));
+    hmm = file.getHMM();
+  }
+
+  @Test(groups = "Functional")
+  public void testGetMatchEmissionProbabilities()
+          throws MalformedURLException, IOException
+  {
+    /*
+     * raw value in file is 3.67403
+     * saved as probability e^-X = 0.05259 
+     */
+    double mep = hmm.getMatchEmissionProbability(0, 'R');
+    assertEquals(mep, 0.02537400637, 0.0001d);
+    assertEquals(mep, Math.pow(Math.E, -3.67403), 0.0001d);
+
+    mep = hmm.getMatchEmissionProbability(19, 'W');
+    assertEquals(mep, 0.00588228492, 0.0001d);
+    assertEquals(mep, Math.pow(Math.E, -5.13581), 0.0001d);
+
+    // column 160 is a gapped region of the model
+    mep = hmm.getMatchEmissionProbability(160, 'G');
+    assertEquals(mep, 0D, 0.0001d);
+
+    mep = hmm.getMatchEmissionProbability(475, 'A');
+    assertEquals(mep, 0.04995163708, 0.0001d);
+    assertEquals(mep, Math.pow(Math.E, -2.99670), 0.0001d);
+  }
+  
+  @Test(groups = "Functional")
+  public void testGetInsertEmissionProbabilities()
+  {
+    double iep = hmm.getInsertEmissionProbability(2, 'A');
+    assertEquals(iep, Math.pow(Math.E, -2.68618), 0.0001d);
+    // symbol is not case-sensitive
+    assertEquals(iep, hmm.getInsertEmissionProbability(2, 'a'));
+
+    iep = hmm.getInsertEmissionProbability(5, 'T');
+    assertEquals(iep, Math.pow(Math.E, -2.77519), 0.0001d);
+
+    // column 161 is gapped in the hmm
+    iep = hmm.getInsertEmissionProbability(161, 'K');
+    assertEquals(iep, 0D, 0.0001d);
+
+    iep = hmm.getInsertEmissionProbability(472, 'L');
+    assertEquals(iep, Math.pow(Math.E, -2.69355), 0.0001d);
+  }
+
+  @Test(groups = "Functional")
+  public void testGetStateTransitionProbabilities()
+  {
+    // * in model file treated as negative infinity
+    double stp = hmm.getStateTransitionProbability(475,
+            HiddenMarkovModel.MATCHTODELETE);
+    assertEquals(stp, Double.NEGATIVE_INFINITY);
+
+    // file value is 5.01631, saved as e^-5.01631
+    stp = hmm.getStateTransitionProbability(8,
+            HiddenMarkovModel.MATCHTOINSERT);
+    assertEquals(stp, Math.pow(Math.E, -5.01631), 0.0001D);
+
+    stp = hmm.getStateTransitionProbability(36,
+            HiddenMarkovModel.MATCHTODELETE);
+    assertEquals(stp, Math.pow(Math.E, -5.73865), 0.0001D);
+
+    stp = hmm.getStateTransitionProbability(22,
+            HiddenMarkovModel.INSERTTOMATCH);
+    assertEquals(stp, Math.pow(Math.E, -0.61958), 0.0001D);
+
+    stp = hmm.getStateTransitionProbability(80,
+            HiddenMarkovModel.INSERTTOINSERT);
+    assertEquals(stp, Math.pow(Math.E, -0.77255), 0.0001D);
+
+    stp = hmm.getStateTransitionProbability(475,
+            HiddenMarkovModel.DELETETOMATCH);
+    assertEquals(stp, 1D, 0.0001D);
+
+    stp = hmm.getStateTransitionProbability(218,
+            HiddenMarkovModel.DELETETODELETE);
+    assertEquals(stp, Math.pow(Math.E, -0.95510), 0.0001D);
+  }
+  
+  @Test(groups = "Functional")
+  public void testGetConsensusSequence()
+  {
+    SequenceI seq = hmm.getConsensusSequence();
+    String subStr = seq.getSequenceAsString().substring(0, 10);
+    assertEquals(subStr, "yelleklGsG");
+    subStr = seq.getSequenceAsString().substring(150, 161);
+    assertEquals(subStr, "-dllk------");
+  }
+
+  /**
+   * A rather pointless test that reproduces the code implemented and asserts
+   * the result is the same...
+   */
+  @Test(groups = "Functional")
+  public void testGetInformationContent()
+  {
+    /*
+     * information measure is sum over all symbols of 
+     * emissionProb * log(emissionProb / background) / log(2)
+     */
+    Map<Character, Float> uniprotFreqs = ResidueProperties.backgroundFrequencies
+            .get("amino");
+    int col = 4;
+    float expected = 0f;
+    for (char aa : hmm.getSymbols().toCharArray())
+    {
+      double mep = hmm.getMatchEmissionProbability(col, aa);
+      float background = uniprotFreqs.get(aa);
+      expected += mep * Math.log(mep / background);
+    }
+    expected /= Math.log(2D);
+
+    float actual = hmm.getInformationContent(col);
+    assertEquals(actual, expected, 0.0001d);
+  }
+}
diff --git a/test/jalview/datamodel/HiddenSequencesTest.java b/test/jalview/datamodel/HiddenSequencesTest.java
index 11b993d..efd71e6 100644
--- a/test/jalview/datamodel/HiddenSequencesTest.java
+++ b/test/jalview/datamodel/HiddenSequencesTest.java
@@ -31,6 +31,7 @@ import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
 
 import jalview.gui.AlignViewport;
 import jalview.gui.JvOptionPane;
+import jalview.viewmodel.AlignmentViewport;
 
 import java.util.List;
 
@@ -487,7 +488,7 @@ public class HiddenSequencesTest
      * represent seqs 2-4 with seq3
      * this hides seq2 and seq4 but not seq3
      */
-    AlignViewport av = new AlignViewport(al);
+    AlignmentViewport av = new AlignViewport(al);
     SequenceGroup sg = new SequenceGroup();
     sg.addSequence(seqs[1], false);
     sg.addSequence(seqs[2], false);
diff --git a/test/jalview/datamodel/VisibleColsIteratorTest.java b/test/jalview/datamodel/RangeElementsIteratorTest.java
similarity index 84%
rename from test/jalview/datamodel/VisibleColsIteratorTest.java
rename to test/jalview/datamodel/RangeElementsIteratorTest.java
index b2d747b..9d14822 100644
--- a/test/jalview/datamodel/VisibleColsIteratorTest.java
+++ b/test/jalview/datamodel/RangeElementsIteratorTest.java
@@ -22,12 +22,13 @@ package jalview.datamodel;
 
 import static org.testng.Assert.assertTrue;
 
+import java.util.Iterator;
 import java.util.NoSuchElementException;
 
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
-public class VisibleColsIteratorTest
+public class RangeElementsIteratorTest
 {
   HiddenColumns hiddenCols;
 
@@ -50,11 +51,12 @@ public class VisibleColsIteratorTest
   @Test(groups = { "Functional" })
   public void testHasNextAndNextWithHidden()
   {
-    VisibleColsIterator it = new VisibleColsIterator(0, 6, hiddenCols);
+    Iterator<Integer> it = hiddenCols.getVisibleColsIterator(0, 6);
     int count = 0;
     while (it.hasNext())
     {
-      it.next();
+      int result = it.next();
+      System.out.println(result);
       count++;
     }
     assertTrue(count == 4, "hasNext() is false after 4 iterations");
@@ -67,8 +69,8 @@ public class VisibleColsIteratorTest
   @Test(groups = { "Functional" })
   public void testHasNextAndNextNoHidden()
   {
-    VisibleColsIterator it2 = new VisibleColsIterator(0, 3,
-            new HiddenColumns());
+    HiddenColumns test = new HiddenColumns();
+    Iterator<Integer> it2 = test.getVisibleColsIterator(0, 3);
     int count = 0;
     while (it2.hasNext())
     {
@@ -85,8 +87,7 @@ public class VisibleColsIteratorTest
   @Test(groups = { "Functional" })
   public void testHasNextAndNextStartHidden()
   {
-    VisibleColsIterator it3 = new VisibleColsIterator(0, 6,
-            hiddenColsAtStart);
+    Iterator<Integer> it3 = hiddenColsAtStart.getVisibleColsIterator(0, 6);
     int count = 0;
     while (it3.hasNext())
     {
@@ -103,7 +104,7 @@ public class VisibleColsIteratorTest
   @Test(groups = { "Functional" })
   public void testHasNextAndNextEndHidden()
   {
-    VisibleColsIterator it4 = new VisibleColsIterator(0, 4, hiddenCols);
+    Iterator<Integer> it4 = hiddenCols.getVisibleColsIterator(0, 4);
     int count = 0;
     while (it4.hasNext())
     {
@@ -123,7 +124,7 @@ public class VisibleColsIteratorTest
     expectedExceptions = { NoSuchElementException.class })
   public void testLastNextWithHidden() throws NoSuchElementException
   {
-    VisibleColsIterator it = new VisibleColsIterator(0, 3, hiddenCols);
+    Iterator<Integer> it = hiddenCols.getVisibleColsIterator(0, 3);
     while (it.hasNext())
     {
       it.next();
@@ -140,8 +141,8 @@ public class VisibleColsIteratorTest
     expectedExceptions = { NoSuchElementException.class })
   public void testLastNextNoHidden() throws NoSuchElementException
   {
-    VisibleColsIterator it2 = new VisibleColsIterator(0, 3,
-            new HiddenColumns());
+    HiddenColumns test = new HiddenColumns();
+    Iterator<Integer> it2 = test.getVisibleColsIterator(0, 3);
     while (it2.hasNext())
     {
       it2.next();
@@ -158,8 +159,7 @@ public class VisibleColsIteratorTest
     expectedExceptions = { NoSuchElementException.class })
   public void testLastNextStartHidden() throws NoSuchElementException
   {
-    VisibleColsIterator it3 = new VisibleColsIterator(0, 6,
-            hiddenColsAtStart);
+    Iterator<Integer> it3 = hiddenColsAtStart.getVisibleColsIterator(0, 6);
     while (it3.hasNext())
     {
       it3.next();
@@ -176,7 +176,7 @@ public class VisibleColsIteratorTest
     expectedExceptions = { NoSuchElementException.class })
   public void testLastNextEndHidden() throws NoSuchElementException
   {
-    VisibleColsIterator it4 = new VisibleColsIterator(0, 4, hiddenCols);
+    Iterator<Integer> it4 = hiddenCols.getVisibleColsIterator(0, 4);
     while (it4.hasNext())
     {
       it4.next();
@@ -192,7 +192,7 @@ public class VisibleColsIteratorTest
     expectedExceptions = { UnsupportedOperationException.class })
   public void testRemove() throws UnsupportedOperationException
   {
-    VisibleColsIterator it = new VisibleColsIterator(0, 3, hiddenCols);
+    Iterator<Integer> it = hiddenCols.getVisibleColsIterator(0, 3);
     it.remove();
   }
 }
diff --git a/test/jalview/datamodel/ResidueCountTest.java b/test/jalview/datamodel/ResidueCountTest.java
index 4eb6dbf..9a8f93d 100644
--- a/test/jalview/datamodel/ResidueCountTest.java
+++ b/test/jalview/datamodel/ResidueCountTest.java
@@ -27,6 +27,8 @@ import static org.testng.Assert.assertTrue;
 import jalview.datamodel.ResidueCount.SymbolCounts;
 import jalview.gui.JvOptionPane;
 
+import java.util.Arrays;
+
 import org.junit.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
@@ -69,6 +71,7 @@ public class ResidueCountTest
     assertEquals(rc.getCount('N'), 1);
     assertEquals(rc.getCount('?'), 0);
     assertEquals(rc.getCount('-'), 0);
+    assertEquals(rc.getTotalResidueCount(), 11);
 
     assertFalse(rc.isCountingInts());
     assertFalse(rc.isUsingOtherData());
@@ -90,6 +93,7 @@ public class ResidueCountTest
     assertEquals(rc.getCount(' '), 4);
     assertEquals(rc.getCount('-'), 4);
     assertEquals(rc.getCount('.'), 4);
+    assertEquals(rc.getTotalResidueCount(), 0);
     assertFalse(rc.isUsingOtherData());
     assertFalse(rc.isCountingInts());
   }
@@ -158,6 +162,7 @@ public class ResidueCountTest
     assertEquals(rc.getCount('m'), 13);
     assertEquals(rc.getCount('G'), 0);
     assertEquals(rc.getCount('-'), 0);
+    assertEquals(rc.getTotalResidueCount(), 27);
 
     assertFalse(rc.isCountingInts());
     assertFalse(rc.isUsingOtherData());
@@ -439,4 +444,23 @@ public class ResidueCountTest
     assertEquals(rc.getCount('?'), 6);
     assertEquals(rc.getCount('!'), 7);
   }
+
+  @Test(groups = "Functional")
+  public void testConstructor_forSequences()
+  {
+    SequenceI seq1 = new Sequence("seq1", "abcde--. FCD");
+    SequenceI seq2 = new Sequence("seq2", "ab.kKqBd-.");
+    ResidueCount rc = new ResidueCount(Arrays.asList(seq1, seq2));
+
+    assertEquals(rc.getGapCount(), 7);
+    assertEquals(rc.getTotalResidueCount(), 15); // excludes gaps
+    assertEquals(rc.getCount('a'), 2);
+    assertEquals(rc.getCount('A'), 2);
+    assertEquals(rc.getCount('B'), 3);
+    assertEquals(rc.getCount('c'), 2);
+    assertEquals(rc.getCount('D'), 3);
+    assertEquals(rc.getCount('f'), 1);
+    assertEquals(rc.getCount('K'), 2);
+    assertEquals(rc.getCount('Q'), 1);
+  }
 }
diff --git a/test/jalview/datamodel/SequenceGroupTest.java b/test/jalview/datamodel/SequenceGroupTest.java
index b0af5c8..df88268 100644
--- a/test/jalview/datamodel/SequenceGroupTest.java
+++ b/test/jalview/datamodel/SequenceGroupTest.java
@@ -16,10 +16,10 @@ import jalview.schemes.PIDColourScheme;
 import java.awt.Color;
 import java.util.Collections;
 
-import junit.extensions.PA;
-
 import org.testng.annotations.Test;
 
+import junit.extensions.PA;
+
 public class SequenceGroupTest
 {
   @Test(groups={"Functional"})
@@ -242,7 +242,7 @@ public class SequenceGroupTest
     sg.setDisplayBoxes(false);
     sg.setDisplayText(false);
     sg.setColourText(true);
-    sg.isDefined = true;
+    PA.setValue(sg, "isDefined", true);
     sg.setShowNonconserved(true);
     sg.setOutlineColour(Color.red);
     sg.setIdColour(Color.blue);
@@ -275,7 +275,7 @@ public class SequenceGroupTest
     assertEquals(sg2.thresholdTextColour, sg.thresholdTextColour);
     assertEquals(sg2.textColour, sg.textColour);
     assertEquals(sg2.textColour2, sg.textColour2);
-    assertEquals(sg2.getIgnoreGapsConsensus(), sg.getIgnoreGapsConsensus());
+    assertEquals(sg2.isIgnoreGapsConsensus(), sg.isIgnoreGapsConsensus());
     assertEquals(sg2.isShowSequenceLogo(), sg.isShowSequenceLogo());
     assertEquals(sg2.isNormaliseSequenceLogo(),
             sg.isNormaliseSequenceLogo());
diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index a084a8e..5a14514 100644
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -28,6 +28,7 @@ import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.analysis.AlignmentGenerator;
 import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
 import jalview.datamodel.PDBEntry.Type;
@@ -38,16 +39,17 @@ import java.io.File;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.BitSet;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Vector;
 
-import junit.extensions.PA;
-
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
+import junit.extensions.PA;
+
 public class SequenceTest
 {
 
@@ -799,7 +801,7 @@ public class SequenceTest
     Assert.assertEquals(pdbe1a,
             sq.getDatasetSequence().getPDBEntry("1PDB"),
             "PDB Entry '1PDB' not found on dataset sequence via getPDBEntry.");
-    ArrayList<Annotation> annotsList = new ArrayList<Annotation>();
+    ArrayList<Annotation> annotsList = new ArrayList<>();
     System.out.println(">>>>>> " + sq.getSequenceAsString().length());
     annotsList.add(new Annotation("A", "A", 'X', 0.1f));
     annotsList.add(new Annotation("A", "A", 'X', 0.1f));
@@ -1674,6 +1676,20 @@ public class SequenceTest
   }
 
   @Test(groups = { "Functional" })
+  public void testGapBitset()
+  {
+    SequenceI sq = new Sequence("test/8-13", "-ABC---DE-F--");
+    BitSet bs = sq.gapBitset();
+    BitSet expected = new BitSet();
+    expected.set(0);
+    expected.set(4, 7);
+    expected.set(9);
+    expected.set(11, 13);
+
+    assertTrue(bs.equals(expected));
+
+  }
+
   public void testFindFeatures_largeEndPos()
   {
     /*
@@ -1881,4 +1897,162 @@ public class SequenceTest
     assertEquals(8, sq.getDatasetSequence().getStart());
     assertEquals(9, sq.getDatasetSequence().getEnd());
   }
+
+  /**
+   * Test the code used to locate the reference sequence ruler origin
+   */
+  @Test(groups = { "Functional" })
+  public void testLocateVisibleStartofSequence()
+  {
+    // create random alignment
+    AlignmentGenerator gen = new AlignmentGenerator(false);
+    AlignmentI al = gen.generate(50, 20, 123, 5, 5);
+
+    HiddenColumns cs = al.getHiddenColumns();
+    ColumnSelection colsel = new ColumnSelection();
+
+    SequenceI seq = new Sequence("RefSeq", "-A-SD-ASD--E---");
+    assertEquals(2, seq.findIndex(seq.getStart()));
+
+    // no hidden columns
+    assertEquals(seq.findIndex(seq.getStart()) - 1,
+            seq.firstResidueOutsideIterator(cs.iterator()));
+
+    // hidden column on gap after end of sequence - should not affect bounds
+    colsel.hideSelectedColumns(13, al.getHiddenColumns());
+    assertEquals(seq.findIndex(seq.getStart()) - 1,
+            seq.firstResidueOutsideIterator(cs.iterator()));
+
+    cs.revealAllHiddenColumns(colsel);
+    // hidden column on gap before beginning of sequence - should vis bounds by
+    // one
+    colsel.hideSelectedColumns(0, al.getHiddenColumns());
+    assertEquals(seq.findIndex(seq.getStart()) - 2,
+            cs.absoluteToVisibleColumn(
+                    seq.firstResidueOutsideIterator(cs.iterator())));
+
+    cs.revealAllHiddenColumns(colsel);
+    // hide columns around most of sequence - leave one residue remaining
+    cs.hideColumns(1, 3);
+    cs.hideColumns(6, 11);
+
+    Iterator<int[]> it = cs.getVisContigsIterator(0, 6, false);
+
+    assertEquals("-D", seq.getSequenceStringFromIterator(it));
+    // cs.getVisibleSequenceStrings(0, 5, new SequenceI[]
+    // { seq })[0]);
+
+    assertEquals(4, seq.firstResidueOutsideIterator(cs.iterator()));
+    cs.revealAllHiddenColumns(colsel);
+
+    // hide whole sequence - should just get location of hidden region
+    // containing sequence
+    cs.hideColumns(1, 11);
+    assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
+
+    cs.revealAllHiddenColumns(colsel);
+    cs.hideColumns(0, 15);
+    assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
+
+    SequenceI seq2 = new Sequence("RefSeq2", "-------A-SD-ASD--E---");
+
+    cs.revealAllHiddenColumns(colsel);
+    cs.hideColumns(7, 17);
+    assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator()));
+
+    cs.revealAllHiddenColumns(colsel);
+    cs.hideColumns(3, 17);
+    assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator()));
+
+    cs.revealAllHiddenColumns(colsel);
+    cs.hideColumns(3, 19);
+    assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator()));
+
+    cs.revealAllHiddenColumns(colsel);
+    cs.hideColumns(0, 0);
+    assertEquals(1, seq.firstResidueOutsideIterator(cs.iterator()));
+
+    cs.revealAllHiddenColumns(colsel);
+    cs.hideColumns(0, 1);
+    assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
+
+    cs.revealAllHiddenColumns(colsel);
+    cs.hideColumns(0, 2);
+    assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
+
+    cs.revealAllHiddenColumns(colsel);
+    cs.hideColumns(1, 1);
+    assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
+
+    cs.revealAllHiddenColumns(colsel);
+    cs.hideColumns(1, 2);
+    assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
+
+    cs.revealAllHiddenColumns(colsel);
+    cs.hideColumns(1, 3);
+    assertEquals(4, seq.firstResidueOutsideIterator(cs.iterator()));
+
+    cs.revealAllHiddenColumns(colsel);
+    cs.hideColumns(0, 2);
+    cs.hideColumns(5, 6);
+    assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
+
+    cs.revealAllHiddenColumns(colsel);
+    cs.hideColumns(0, 2);
+    cs.hideColumns(5, 6);
+    cs.hideColumns(9, 10);
+    assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
+
+    cs.revealAllHiddenColumns(colsel);
+    cs.hideColumns(0, 2);
+    cs.hideColumns(7, 11);
+    assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
+
+    cs.revealAllHiddenColumns(colsel);
+    cs.hideColumns(2, 4);
+    cs.hideColumns(7, 11);
+    assertEquals(1, seq.firstResidueOutsideIterator(cs.iterator()));
+
+    cs.revealAllHiddenColumns(colsel);
+    cs.hideColumns(2, 4);
+    cs.hideColumns(7, 12);
+    assertEquals(1, seq.firstResidueOutsideIterator(cs.iterator()));
+
+    cs.revealAllHiddenColumns(colsel);
+    cs.hideColumns(1, 11);
+    assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
+
+    cs.revealAllHiddenColumns(colsel);
+    cs.hideColumns(0, 12);
+    assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
+
+    cs.revealAllHiddenColumns(colsel);
+    cs.hideColumns(0, 4);
+    cs.hideColumns(6, 12);
+    assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
+
+    cs.revealAllHiddenColumns(colsel);
+    cs.hideColumns(0, 1);
+    cs.hideColumns(3, 12);
+    assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
+
+    cs.revealAllHiddenColumns(colsel);
+    cs.hideColumns(3, 14);
+    cs.hideColumns(17, 19);
+    assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator()));
+
+    cs.revealAllHiddenColumns(colsel);
+    cs.hideColumns(3, 7);
+    cs.hideColumns(9, 14);
+    cs.hideColumns(17, 19);
+    assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator()));
+
+    cs.revealAllHiddenColumns(colsel);
+    cs.hideColumns(0, 1);
+    cs.hideColumns(3, 4);
+    cs.hideColumns(6, 8);
+    cs.hideColumns(10, 12);
+    assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
+
+  }
 }
diff --git a/test/jalview/datamodel/StartRegionIteratorTest.java b/test/jalview/datamodel/StartRegionIteratorTest.java
new file mode 100644
index 0000000..23d0b00
--- /dev/null
+++ b/test/jalview/datamodel/StartRegionIteratorTest.java
@@ -0,0 +1,214 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.datamodel;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertTrue;
+
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
+import org.testng.annotations.Test;
+
+public class StartRegionIteratorTest
+{
+  /**
+   * Test the start region iterator
+   */
+  @Test(groups = { "Functional" })
+  public void testBasicBoundsIterator()
+  {
+    List<int[]> hiddenColumns = null;
+
+    // null hidden columns
+    Iterator<Integer> it = new StartRegionIterator(3, 10,
+            hiddenColumns);
+    assertFalse(it.hasNext());
+
+    hiddenColumns = new ArrayList<>();
+
+    // no hidden columns
+    it = new StartRegionIterator(3, 10, hiddenColumns);
+    assertFalse(it.hasNext());
+
+    // add some hidden columns
+    hiddenColumns.add(new int[] { 5, 10 });
+    hiddenColumns.add(new int[] { 25, 40 });
+
+    it = new StartRegionIterator(3, 10, hiddenColumns);
+    assertTrue(it.hasNext());
+    Integer result = it.next();
+    assertEquals(5, (int) result);
+    assertFalse(it.hasNext());
+
+    it = new StartRegionIterator(3, 15, hiddenColumns);
+    assertTrue(it.hasNext());
+    result = it.next();
+    assertEquals(5, (int) result);
+    assertFalse(it.hasNext());
+
+    it = new StartRegionIterator(3, 18, hiddenColumns);
+    assertTrue(it.hasNext());
+    result = it.next();
+    assertEquals(5, (int) result);
+    assertFalse(it.hasNext());
+
+    it = new StartRegionIterator(3, 19, hiddenColumns);
+    assertTrue(it.hasNext());
+    result = it.next();
+    assertEquals(5, (int) result);
+    assertTrue(it.hasNext());
+    result = it.next();
+    assertEquals(19, (int) result);
+    assertFalse(it.hasNext());
+
+    hiddenColumns.add(new int[] { 47, 50 });
+
+    it = new StartRegionIterator(15, 60, hiddenColumns);
+    assertTrue(it.hasNext());
+    result = it.next();
+    assertEquals(19, (int) result);
+    assertTrue(it.hasNext());
+    result = it.next();
+    assertEquals(25, (int) result);
+    assertFalse(it.hasNext());
+  }
+
+  /**
+   * Test the start region iterator with null cursor
+   */
+  @Test(groups = { "Functional" })
+  public void testBoundsIteratorUsingNullCursor()
+  {
+    List<int[]> hiddenColumns = null;
+    HiddenCursorPosition pos = null;
+
+    // null hidden columns
+    Iterator<Integer> it = new StartRegionIterator(pos, 3, 10,
+            hiddenColumns);
+    assertFalse(it.hasNext());
+
+    hiddenColumns = new ArrayList<>();
+
+    // no hidden columns
+    it = new StartRegionIterator(pos, 3, 10, hiddenColumns);
+    assertFalse(it.hasNext());
+
+    // add some hidden columns
+    hiddenColumns.add(new int[] { 5, 10 });
+    hiddenColumns.add(new int[] { 25, 40 });
+
+    it = new StartRegionIterator(pos, 3, 10, hiddenColumns);
+    assertTrue(it.hasNext());
+    Integer result = it.next();
+    assertEquals(5, (int) result);
+    assertFalse(it.hasNext());
+
+    it = new StartRegionIterator(pos, 3, 15, hiddenColumns);
+    assertTrue(it.hasNext());
+    result = it.next();
+    assertEquals(5, (int) result);
+    assertFalse(it.hasNext());
+
+    it = new StartRegionIterator(pos, 3, 18, hiddenColumns);
+    assertTrue(it.hasNext());
+    result = it.next();
+    assertEquals(5, (int) result);
+    assertFalse(it.hasNext());
+
+    it = new StartRegionIterator(pos, 3, 19, hiddenColumns);
+    assertTrue(it.hasNext());
+    result = it.next();
+    assertEquals(5, (int) result);
+    assertTrue(it.hasNext());
+    result = it.next();
+    assertEquals(19, (int) result);
+    assertFalse(it.hasNext());
+
+    hiddenColumns.add(new int[] { 47, 50 });
+
+    it = new StartRegionIterator(pos, 15, 60, hiddenColumns);
+    assertTrue(it.hasNext());
+    result = it.next();
+    assertEquals(19, (int) result);
+    assertTrue(it.hasNext());
+    result = it.next();
+    assertEquals(25, (int) result);
+    assertFalse(it.hasNext());
+  }
+
+  /**
+   * Test the start region iterator with nonnull cursor
+   */
+  @Test(groups = { "Functional" })
+  public void testBoundsIteratorUsingCursor()
+  {
+    List<int[]> hiddenColumns = new ArrayList<>();
+
+    // add some hidden columns
+    hiddenColumns.add(new int[] { 5, 10 });
+    hiddenColumns.add(new int[] { 25, 40 });
+
+    HiddenCursorPosition pos = new HiddenCursorPosition(0, 0);
+
+    Iterator<Integer> it = new StartRegionIterator(pos, 3, 10,
+            hiddenColumns);
+    assertTrue(it.hasNext());
+    Integer result = it.next();
+    assertEquals(5, (int) result);
+    assertFalse(it.hasNext());
+
+    it = new StartRegionIterator(pos, 3, 15, hiddenColumns);
+    assertTrue(it.hasNext());
+    result = it.next();
+    assertEquals(5, (int) result);
+    assertFalse(it.hasNext());
+
+    it = new StartRegionIterator(pos, 3, 18, hiddenColumns);
+    assertTrue(it.hasNext());
+    result = it.next();
+    assertEquals(5, (int) result);
+    assertFalse(it.hasNext());
+
+    it = new StartRegionIterator(pos, 3, 19, hiddenColumns);
+    assertTrue(it.hasNext());
+    result = it.next();
+    assertEquals(5, (int) result);
+    assertTrue(it.hasNext());
+    result = it.next();
+    assertEquals(19, (int) result);
+    assertFalse(it.hasNext());
+
+    pos = new HiddenCursorPosition(1, 6);
+    hiddenColumns.add(new int[] { 47, 50 });
+
+    it = new StartRegionIterator(pos, 15, 60, hiddenColumns);
+    assertTrue(it.hasNext());
+    result = it.next();
+    assertEquals(19, (int) result);
+    assertTrue(it.hasNext());
+    result = it.next();
+    assertEquals(25, (int) result);
+    assertFalse(it.hasNext());
+  }
+}
diff --git a/test/jalview/datamodel/VisibleContigsIteratorTest.java b/test/jalview/datamodel/VisibleContigsIteratorTest.java
new file mode 100644
index 0000000..8f31dae
--- /dev/null
+++ b/test/jalview/datamodel/VisibleContigsIteratorTest.java
@@ -0,0 +1,223 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.datamodel;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertTrue;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.testng.annotations.Test;
+
+public class VisibleContigsIteratorTest
+{
+  /**
+   * Test the iterator with single visible regions
+   */
+  @Test(groups = { "Functional" })
+  public void testSimpleVisibleRegions()
+  {
+    List<int[]> hiddenColumns = null;
+
+    // null hidden columns
+    VisibleContigsIterator it = new VisibleContigsIterator(3, 10,
+            hiddenColumns);
+    assertTrue(it.hasNext());
+    assertFalse(it.endsAtHidden());
+    int[] result = it.next();
+    assertEquals(3, result[0]);
+    assertEquals(9, result[1]);
+    assertFalse(it.hasNext());
+    assertFalse(it.endsAtHidden());
+
+    hiddenColumns = new ArrayList<>();
+
+    // no hidden columns
+    it = new VisibleContigsIterator(3, 10,
+            hiddenColumns);
+    assertTrue(it.hasNext());
+    assertFalse(it.endsAtHidden());
+    result = it.next();
+    assertEquals(3, result[0]);
+    assertEquals(9, result[1]);
+    assertFalse(it.hasNext());
+    assertFalse(it.endsAtHidden());
+
+    // hidden columns, but not where we are looking
+    hiddenColumns.add(new int[] { 5, 10 });
+    hiddenColumns.add(new int[] { 25, 40 });
+
+    it = new VisibleContigsIterator(2, 3, hiddenColumns);
+    assertTrue(it.hasNext());
+    assertFalse(it.endsAtHidden());
+    result = it.next();
+    assertEquals(2, result[0]);
+    assertEquals(2, result[1]);
+    assertFalse(it.hasNext());
+    assertFalse(it.endsAtHidden());
+
+    it = new VisibleContigsIterator(5, 7, hiddenColumns);
+    assertFalse(it.hasNext());
+    assertFalse(it.endsAtHidden());
+
+    it = new VisibleContigsIterator(11, 15, hiddenColumns);
+    assertTrue(it.hasNext());
+    assertFalse(it.endsAtHidden());
+    result = it.next();
+    assertEquals(11, result[0]);
+    assertEquals(14, result[1]);
+    assertFalse(it.hasNext());
+    assertFalse(it.endsAtHidden());
+
+    it = new VisibleContigsIterator(50, 60, hiddenColumns);
+    assertTrue(it.hasNext());
+    assertFalse(it.endsAtHidden());
+    result = it.next();
+    assertEquals(50, result[0]);
+    assertEquals(59, result[1]);
+    assertFalse(it.hasNext());
+    assertFalse(it.endsAtHidden());
+  }
+
+  /**
+   * Test the iterator with multiple visible regions
+   */
+  @Test(groups = { "Functional" })
+  public void testMultipleVisibleRegions()
+  {
+    List<int[]> hiddenColumns = new ArrayList<>();
+    hiddenColumns.add(new int[] { 5, 10 });
+    hiddenColumns.add(new int[] { 25, 40 });
+
+    // all hidden columns covered
+    VisibleContigsIterator it = new VisibleContigsIterator(3, 50,
+            hiddenColumns);
+    assertTrue(it.hasNext());
+    assertFalse(it.endsAtHidden());
+    int[] result = it.next();
+    assertEquals(3, result[0]);
+    assertEquals(4, result[1]);
+
+    assertTrue(it.hasNext());
+    assertFalse(it.endsAtHidden());
+    result = it.next();
+    assertEquals(11, result[0]);
+    assertEquals(24, result[1]);
+
+    assertTrue(it.hasNext());
+    assertFalse(it.endsAtHidden());
+    result = it.next();
+    assertEquals(41, result[0]);
+    assertEquals(49, result[1]);
+
+    assertFalse(it.hasNext());
+    assertFalse(it.endsAtHidden());
+  }
+
+  /**
+   * Test the iterator with regions which start/end at hidden region edges
+   */
+  @Test(groups = { "Functional" })
+  public void testVisibleRegionsAtHiddenEdges()
+  {
+    List<int[]> hiddenColumns = new ArrayList<>();
+    hiddenColumns.add(new int[] { 5, 10 });
+    hiddenColumns.add(new int[] { 25, 40 });
+
+    VisibleContigsIterator it = new VisibleContigsIterator(0, 10,
+            hiddenColumns);
+    assertTrue(it.hasNext());
+    assertTrue(it.endsAtHidden());
+    int[] result = it.next();
+    assertEquals(0, result[0]);
+    assertEquals(4, result[1]);
+    assertFalse(it.hasNext());
+    assertTrue(it.endsAtHidden());
+
+    it = new VisibleContigsIterator(2, 11, hiddenColumns);
+    assertTrue(it.hasNext());
+    assertTrue(it.endsAtHidden());
+    result = it.next();
+    assertEquals(2, result[0]);
+    assertEquals(4, result[1]);
+    assertFalse(it.hasNext());
+    assertTrue(it.endsAtHidden());
+
+    it = new VisibleContigsIterator(2, 12, hiddenColumns);
+    assertTrue(it.hasNext());
+    assertFalse(it.endsAtHidden());
+    result = it.next();
+    assertEquals(2, result[0]);
+    assertEquals(4, result[1]);
+    assertTrue(it.hasNext());
+    assertFalse(it.endsAtHidden());
+    result = it.next();
+    assertEquals(11, result[0]);
+    assertEquals(11, result[1]);
+    assertFalse(it.hasNext());
+    assertFalse(it.endsAtHidden());
+
+    it = new VisibleContigsIterator(13, 25, hiddenColumns);
+    assertTrue(it.hasNext());
+    assertFalse(it.endsAtHidden());
+    result = it.next();
+    assertEquals(13, result[0]);
+    assertEquals(24, result[1]);
+    assertFalse(it.hasNext());
+
+    it = new VisibleContigsIterator(13, 26, hiddenColumns);
+    assertTrue(it.hasNext());
+    assertTrue(it.endsAtHidden());
+    result = it.next();
+    assertEquals(13, result[0]);
+    assertEquals(24, result[1]);
+    assertFalse(it.hasNext());
+
+    it = new VisibleContigsIterator(13, 27, hiddenColumns);
+    assertTrue(it.hasNext());
+    assertTrue(it.endsAtHidden());
+    result = it.next();
+    assertEquals(13, result[0]);
+    assertEquals(24, result[1]);
+    assertFalse(it.hasNext());
+
+    it = new VisibleContigsIterator(13, 41, hiddenColumns);
+    assertTrue(it.hasNext());
+    assertTrue(it.endsAtHidden());
+    result = it.next();
+    assertEquals(13, result[0]);
+    assertEquals(24, result[1]);
+    assertFalse(it.hasNext());
+
+    it = new VisibleContigsIterator(13, 42, hiddenColumns);
+    assertTrue(it.hasNext());
+    assertFalse(it.endsAtHidden());
+    result = it.next();
+    assertEquals(13, result[0]);
+    assertEquals(24, result[1]);
+    assertTrue(it.hasNext());
+    result = it.next();
+    assertEquals(41, result[0]);
+    assertEquals(41, result[1]);
+  }
+}
diff --git a/test/jalview/ext/ensembl/EnsemblGeneTest.java b/test/jalview/ext/ensembl/EnsemblGeneTest.java
index 1b1a2b4..217742d 100644
--- a/test/jalview/ext/ensembl/EnsemblGeneTest.java
+++ b/test/jalview/ext/ensembl/EnsemblGeneTest.java
@@ -25,6 +25,7 @@ import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.api.FeatureSettingsModelI;
+import jalview.bin.Cache;
 import jalview.datamodel.SequenceDummy;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
@@ -53,6 +54,7 @@ public class EnsemblGeneTest
   @BeforeClass(alwaysRun = true)
   public void setUp()
   {
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
     SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
   }
 
diff --git a/test/jalview/ext/jmol/JmolCommandsTest.java b/test/jalview/ext/jmol/JmolCommandsTest.java
index 3309adf..e42b54f 100644
--- a/test/jalview/ext/jmol/JmolCommandsTest.java
+++ b/test/jalview/ext/jmol/JmolCommandsTest.java
@@ -115,7 +115,7 @@ public class JmolCommandsTest
     String chainACommand = commands[0].commands[0];
     // M colour is #82827d == (130, 130, 125) (see strand.html help page)
     assertTrue(chainACommand
-            .contains(";select 21:A/1.1;color[130,130,125]"));
+            .contains("select 21:A/1.1;color[130,130,125]")); // first one
     // H colour is #60609f == (96, 96, 159)
     assertTrue(chainACommand.contains(";select 22:A/1.1;color[96,96,159]"));
     // hidden columns are Gray (128, 128, 128)
@@ -128,7 +128,7 @@ public class JmolCommandsTest
     String chainBCommand = commands[1].commands[0];
     // M colour is #82827d == (130, 130, 125)
     assertTrue(chainBCommand
-            .contains(";select 21:B/2.1;color[130,130,125]"));
+            .contains("select 21:B/2.1;color[130,130,125]"));
     // V colour is #ffff00 == (255, 255, 0)
     assertTrue(chainBCommand
 .contains(";select 22:B/2.1;color[255,255,0]"));
diff --git a/test/jalview/gui/AlignFrameTest.java b/test/jalview/gui/AlignFrameTest.java
index 1ee25c7..0f15ce4 100644
--- a/test/jalview/gui/AlignFrameTest.java
+++ b/test/jalview/gui/AlignFrameTest.java
@@ -26,11 +26,13 @@ import static org.testng.Assert.assertNotSame;
 import static org.testng.Assert.assertSame;
 import static org.testng.Assert.assertTrue;
 
+import jalview.api.AlignViewportI;
 import jalview.api.FeatureColourI;
 import jalview.bin.Cache;
 import jalview.bin.Jalview;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
@@ -46,9 +48,10 @@ import jalview.schemes.JalviewColourScheme;
 import jalview.schemes.StrandColourScheme;
 import jalview.schemes.TurnColourScheme;
 import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
 
 import java.awt.Color;
-import java.util.List;
+import java.util.Iterator;
 
 import org.testng.annotations.AfterMethod;
 import org.testng.annotations.BeforeClass;
@@ -92,21 +95,25 @@ public class AlignFrameTest
      */
     assertFalse(alignFrame.hideFeatureColumns("exon", true));
     assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
-    assertTrue(alignFrame.getViewport().getAlignment().getHiddenColumns()
-            .getHiddenColumnsCopy().isEmpty());
+
+    assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
+            .getNumberOfRegions(), 0);
+
     assertFalse(alignFrame.hideFeatureColumns("exon", false));
     assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
-    assertTrue(alignFrame.getViewport().getAlignment().getHiddenColumns()
-            .getHiddenColumnsCopy().isEmpty());
+
+    assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
+            .getNumberOfRegions(), 0);
 
     /*
      * hiding a feature in all columns does nothing
      */
     assertFalse(alignFrame.hideFeatureColumns("Metal", true));
     assertTrue(alignFrame.getViewport().getColumnSelection().isEmpty());
-    List<int[]> hidden = alignFrame.getViewport().getAlignment()
-            .getHiddenColumns().getHiddenColumnsCopy();
-    assertTrue(hidden.isEmpty());
+
+    assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
+            .getNumberOfRegions(), 0);
+
 
     /*
      * threshold Metal to hide features where score < 5
@@ -118,11 +125,12 @@ public class AlignFrameTest
     fc.setThreshold(5f);
     alignFrame.getFeatureRenderer().setColour("Metal", fc);
     assertTrue(alignFrame.hideFeatureColumns("Metal", true));
-    hidden = alignFrame.getViewport().getAlignment().getHiddenColumns()
-            .getHiddenColumnsCopy();
-    assertEquals(hidden.size(), 1);
-    assertEquals(hidden.get(0)[0], 5);
-    assertEquals(hidden.get(0)[1], 9);
+    HiddenColumns hidden = alignFrame.getViewport().getAlignment().getHiddenColumns();
+    assertEquals(hidden.getNumberOfRegions(), 1);
+    Iterator<int[]> regions = hidden.iterator();
+    int[] next = regions.next();
+    assertEquals(next[0], 5);
+    assertEquals(next[1], 9);
 
     /*
      * hide a feature present in some columns
@@ -131,13 +139,16 @@ public class AlignFrameTest
      */
     alignFrame.getViewport().showAllHiddenColumns();
     assertTrue(alignFrame.hideFeatureColumns("Turn", true));
-    hidden = alignFrame.getViewport().getAlignment().getHiddenColumns()
-            .getHiddenColumnsCopy();
-    assertEquals(hidden.size(), 2);
-    assertEquals(hidden.get(0)[0], 1);
-    assertEquals(hidden.get(0)[1], 3);
-    assertEquals(hidden.get(1)[0], 6);
-    assertEquals(hidden.get(1)[1], 8);
+    regions = alignFrame.getViewport().getAlignment()
+            .getHiddenColumns().iterator();
+    assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
+            .getNumberOfRegions(), 2);
+    next = regions.next();
+    assertEquals(next[0], 1);
+    assertEquals(next[1], 3);
+    next = regions.next();
+    assertEquals(next[0], 6);
+    assertEquals(next[1], 8);
   }
 
   @BeforeClass(alwaysRun = true)
@@ -199,7 +210,7 @@ public class AlignFrameTest
   @Test(groups = "Functional")
   public void testChangeColour_background_groupsAndThresholds()
   {
-    AlignViewport av = af.getViewport();
+    AlignViewportI av = af.getViewport();
     AlignmentI al = av.getAlignment();
 
     /*
@@ -330,7 +341,7 @@ public class AlignFrameTest
   @Test(groups = "Functional")
   public void testColourThresholdActions()
   {
-    AlignViewport av = af.getViewport();
+    AlignViewportI av = af.getViewport();
     AlignmentI al = av.getAlignment();
 
     /*
@@ -499,7 +510,7 @@ public class AlignFrameTest
   @Test(groups = "Functional")
   public void testNewView_colourThresholds()
   {
-    AlignViewport av = af.getViewport();
+    AlignViewportI av = af.getViewport();
     AlignmentI al = av.getAlignment();
 
     /*
@@ -563,7 +574,7 @@ public class AlignFrameTest
      */
     af.newView_actionPerformed(null);
     assertEquals(af.alignPanel.getViewName(), "View 1");
-    AlignViewport av2 = af.getViewport();
+    AlignmentViewport av2 = af.getViewport();
     assertNotSame(av, av2);
     assertSame(av2, af.alignPanel.av);
     rs = av2.getResidueShading();
diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java
index 5ed0cac..6ab2622 100644
--- a/test/jalview/gui/AlignViewportTest.java
+++ b/test/jalview/gui/AlignViewportTest.java
@@ -26,6 +26,7 @@ import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.api.AlignViewportI;
 import jalview.bin.Cache;
 import jalview.bin.Jalview;
 import jalview.datamodel.AlignedCodonFrame;
@@ -33,8 +34,6 @@ import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.PDBEntry.Type;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.Sequence;
@@ -46,6 +45,7 @@ import jalview.schemes.ColourSchemeI;
 import jalview.schemes.PIDColourScheme;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MapList;
+import jalview.viewmodel.AlignmentViewport;
 import jalview.viewmodel.ViewportRanges;
 
 import java.util.ArrayList;
@@ -68,7 +68,7 @@ public class AlignViewportTest
 
   AlignmentI al;
 
-  AlignViewport testee;
+  AlignmentViewport testee;
 
   @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
@@ -355,7 +355,7 @@ public class AlignViewportTest
   {
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/uniref50.fa", DataSourceType.FILE);
-    AlignViewport av = af.getViewport();
+    AlignViewportI av = af.getViewport();
     SequenceGroup sg1 = new SequenceGroup();
     SequenceGroup sg2 = new SequenceGroup();
     SequenceGroup sg3 = new SequenceGroup();
@@ -384,8 +384,8 @@ public class AlignViewportTest
     jalview.bin.Cache.setProperty("SHOW_OCCUPANCY", Boolean.FALSE.toString());
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/uniref50.fa", DataSourceType.FILE);
-    AlignViewport av = af.getViewport();
-    Assert.assertNull(av.getAlignmentGapAnnotation(), "Preference did not disable occupancy row.");
+    AlignViewportI av = af.getViewport();
+    Assert.assertNull(av.getOccupancyAnnotation(), "Preference did not disable occupancy row.");
     int c = 0;
     for (AlignmentAnnotation aa : av.getAlignment().findAnnotations(null,
             null, "Occupancy"))
@@ -399,10 +399,10 @@ public class AlignViewportTest
     af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/uniref50.fa", DataSourceType.FILE);
     av = af.getViewport();
-    Assert.assertNotNull(av.getAlignmentGapAnnotation(), "Preference did not enable occupancy row.");
+    Assert.assertNotNull(av.getOccupancyAnnotation(), "Preference did not enable occupancy row.");
     c = 0;
     for (AlignmentAnnotation aa : av.getAlignment().findAnnotations(null,
-            null, av.getAlignmentGapAnnotation().label))
+            null, av.getOccupancyAnnotation().label))
     {
       c++;
     }
@@ -423,7 +423,7 @@ public class AlignViewportTest
     String fasta = ">s1\nA-C\n>s2\nA-C\n>s3\nA-D\n>s4\n--D\n";
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(fasta,
             DataSourceType.PASTE);
-    AlignViewport testme = af.getViewport();
+    AlignmentViewport testme = af.getViewport();
     SequenceI cons = testme.getConsensusSeq();
     assertEquals("A-C", cons.getSequenceAsString());
   }
diff --git a/test/jalview/gui/AnnotationColumnChooserTest.java b/test/jalview/gui/AnnotationColumnChooserTest.java
index 06478d5..912cd27 100644
--- a/test/jalview/gui/AnnotationColumnChooserTest.java
+++ b/test/jalview/gui/AnnotationColumnChooserTest.java
@@ -35,7 +35,7 @@ import jalview.io.FileFormat;
 import jalview.io.FormatAdapter;
 
 import java.io.IOException;
-import java.util.List;
+import java.util.Iterator;
 
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
@@ -141,18 +141,21 @@ public class AnnotationColumnChooserTest
 
     HiddenColumns currentHidden = af.getViewport().getAlignment()
             .getHiddenColumns();
-    List<int[]> regions = currentHidden.getHiddenColumnsCopy();
-    assertEquals(regions.get(0)[0], 0);
-    assertEquals(regions.get(0)[1], 3);
-    assertEquals(regions.get(1)[0], 22);
-    assertEquals(regions.get(1)[1], 25);
+    Iterator<int[]> regions = currentHidden.iterator();
+    int[] next = regions.next();
+    assertEquals(0, next[0]);
+    assertEquals(3, next[1]);
+    next = regions.next();
+    assertEquals(22, next[0]);
+    assertEquals(25, next[1]);
 
     // now reset hidden columns
     acc.reset();
     currentHidden = af.getViewport().getAlignment().getHiddenColumns();
-    regions = currentHidden.getHiddenColumnsCopy();
-    assertEquals(regions.get(0)[0], 10);
-    assertEquals(regions.get(0)[1], 20);
+    regions = currentHidden.iterator();
+    next = regions.next();
+    assertEquals(10, next[0]);
+    assertEquals(20, next[1]);
 
     // check works with empty hidden columns as old columns
     oldhidden = new HiddenColumns();
@@ -169,8 +172,9 @@ public class AnnotationColumnChooserTest
 
     acc.reset();
     currentHidden = af.getViewport().getAlignment().getHiddenColumns();
-    regions = currentHidden.getHiddenColumnsCopy();
-    assertEquals(regions.get(0)[0], 10);
-    assertEquals(regions.get(0)[1], 20);
+    regions = currentHidden.iterator();
+    next = regions.next();
+    assertEquals(10, next[0]);
+    assertEquals(20, next[1]);
   }
 }
diff --git a/test/jalview/gui/PairwiseAlignmentPanelTest.java b/test/jalview/gui/PairwiseAlignmentPanelTest.java
index 3322ee8..1ea0ba1 100644
--- a/test/jalview/gui/PairwiseAlignmentPanelTest.java
+++ b/test/jalview/gui/PairwiseAlignmentPanelTest.java
@@ -2,17 +2,19 @@ package jalview.gui;
 
 import static org.testng.Assert.assertEquals;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceGroup;
 import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
+import jalview.viewmodel.AlignmentViewport;
 
 import javax.swing.JTextArea;
 
-import junit.extensions.PA;
-
 import org.testng.annotations.Test;
 
+import junit.extensions.PA;
+
 public class PairwiseAlignmentPanelTest
 {
   @Test(groups = "Functional")
@@ -20,7 +22,7 @@ public class PairwiseAlignmentPanelTest
   {
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/uniref50.fa", DataSourceType.FILE);
-    AlignViewport viewport = af.getViewport();
+    AlignViewportI viewport = af.getViewport();
     AlignmentI al = viewport.getAlignment();
 
     /*
@@ -58,7 +60,7 @@ public class PairwiseAlignmentPanelTest
     String seqs = ">Q93XJ9_SOLTU/23-29\nL-KAISNV\n>FER1_PEA/26-32\nV-TTTKAF\n";
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqs,
             DataSourceType.PASTE);
-    AlignViewport viewport = af.getViewport();
+    AlignViewportI viewport = af.getViewport();
 
     PairwiseAlignPanel testee = new PairwiseAlignPanel(viewport);
 
diff --git a/test/jalview/gui/PopupMenuTest.java b/test/jalview/gui/PopupMenuTest.java
index 40e624d..6f60588 100644
--- a/test/jalview/gui/PopupMenuTest.java
+++ b/test/jalview/gui/PopupMenuTest.java
@@ -30,9 +30,13 @@ import jalview.bin.Cache;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
@@ -46,6 +50,7 @@ import java.awt.Component;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Collections;
+import java.util.Iterator;
 import java.util.List;
 
 import javax.swing.JMenu;
@@ -124,7 +129,7 @@ public class PopupMenuTest
   public void testConfigureReferenceAnnotationsMenu_noSequenceSelected()
   {
     JMenuItem menu = new JMenuItem();
-    List<SequenceI> seqs = new ArrayList<SequenceI>();
+    List<SequenceI> seqs = new ArrayList<>();
     testee.configureReferenceAnnotationsMenu(menu, seqs);
     assertFalse(menu.isEnabled());
     // now try null list
@@ -493,8 +498,8 @@ public class PopupMenuTest
     List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
 
     // create list of links and list of DBRefs
-    List<String> links = new ArrayList<String>();
-    List<DBRefEntry> refs = new ArrayList<DBRefEntry>();
+    List<String> links = new ArrayList<>();
+    List<DBRefEntry> refs = new ArrayList<>();
 
     // links as might be added into Preferences | Connections dialog
     links.add("EMBL-EBI Search | http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$"
@@ -579,7 +584,7 @@ public class PopupMenuTest
     }
 
     // if there are no valid links the Links submenu is disabled
-    List<String> nomatchlinks = new ArrayList<String>();
+    List<String> nomatchlinks = new ArrayList<>();
     nomatchlinks.add("NOMATCH | http://www.uniprot.org/uniprot/$"
             + DB_ACCESSION + "$");
 
@@ -589,4 +594,117 @@ public class PopupMenuTest
     assertFalse(linkMenu.isEnabled());
 
   }
+
+  /**
+   * Test for adding feature links
+   */
+  @Test(groups = { "Functional" })
+  public void testHideInsertions()
+  {
+    // get sequences from the alignment
+    List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
+    
+    // add our own seqs to avoid problems with changes to existing sequences
+    // (gap at end of sequences varies depending on how tests are run!)
+    Sequence seqGap1 = new Sequence("GappySeq",
+            "AAAA----AA-AAAAAAA---AAA-----------AAAAAAAAAA--");
+    seqGap1.createDatasetSequence();
+    seqs.add(seqGap1);
+    Sequence seqGap2 = new Sequence("LessGappySeq",
+            "AAAAAA-AAAAA---AAA--AAAAA--AAAAAAA-AAAAAA");
+    seqGap2.createDatasetSequence();
+    seqs.add(seqGap2);
+    Sequence seqGap3 = new Sequence("AnotherGapSeq",
+            "AAAAAA-AAAAAA--AAAAAA-AAAAAAAAAAA---AAAAAAAA");
+    seqGap3.createDatasetSequence();
+    seqs.add(seqGap3);
+    Sequence seqGap4 = new Sequence("NoGaps",
+            "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA");
+    seqGap4.createDatasetSequence();
+    seqs.add(seqGap4);
+
+    ColumnSelection sel = new ColumnSelection();
+    parentPanel.av.getAlignment().getHiddenColumns()
+            .revealAllHiddenColumns(sel);
+
+    // get the Popup Menu for 7th sequence - no insertions
+    testee = new PopupMenu(parentPanel, seqs.get(7), null);
+    testee.hideInsertions_actionPerformed(null);
+    
+    HiddenColumns hidden = parentPanel.av.getAlignment().getHiddenColumns();
+    Iterator<int[]> it = hidden.iterator();
+    assertFalse(it.hasNext());
+
+    // get the Popup Menu for GappySeq - this time we have insertions
+    testee = new PopupMenu(parentPanel, seqs.get(4), null);
+    testee.hideInsertions_actionPerformed(null);
+    hidden = parentPanel.av.getAlignment().getHiddenColumns();
+    it = hidden.iterator();
+
+    assertTrue(it.hasNext());
+    int[] region = it.next();
+    assertEquals(region[0], 4);
+    assertEquals(region[1], 7);
+
+    assertTrue(it.hasNext());
+    region = it.next();
+    assertEquals(region[0], 10);
+    assertEquals(region[1], 10);
+
+    assertTrue(it.hasNext());
+    region = it.next();
+    assertEquals(region[0], 18);
+    assertEquals(region[1], 20);
+
+    assertTrue(it.hasNext());
+    region = it.next();
+    assertEquals(region[0], 24);
+    assertEquals(region[1], 34);
+
+    assertTrue(it.hasNext());
+    region = it.next();
+    assertEquals(region[0], 45);
+    assertEquals(region[1], 46);
+
+    assertFalse(it.hasNext());
+
+    sel = new ColumnSelection();
+    hidden.revealAllHiddenColumns(sel);
+
+    // make a sequence group and hide insertions within the group
+    SequenceGroup sg = new SequenceGroup();
+    sg.setStartRes(8);
+    sg.setEndRes(42);
+    sg.addSequence(seqGap2, false);
+    sg.addSequence(seqGap3, false);
+    parentPanel.av.setSelectionGroup(sg);
+
+    // hide columns outside and within selection
+    // only hidden columns outside the collection will be retained (unless also
+    // gaps in the selection)
+    hidden.hideColumns(1, 10);
+    hidden.hideColumns(31, 40);
+
+    // get the Popup Menu for LessGappySeq in the sequence group
+    testee = new PopupMenu(parentPanel, seqs.get(5), null);
+    testee.hideInsertions_actionPerformed(null);
+    hidden = parentPanel.av.getAlignment().getHiddenColumns();
+    it = hidden.iterator();
+
+    assertTrue(it.hasNext());
+    region = it.next();
+    assertEquals(region[0], 1);
+    assertEquals(region[1], 7);
+
+    assertTrue(it.hasNext());
+    region = it.next();
+    assertEquals(region[0], 13);
+    assertEquals(region[1], 14);
+
+    assertTrue(it.hasNext());
+    region = it.next();
+    assertEquals(region[0], 34);
+    assertEquals(region[1], 34);
+  }
+
 }
diff --git a/test/jalview/gui/SequenceRendererTest.java b/test/jalview/gui/SequenceRendererTest.java
index 359377a..d3d6476 100644
--- a/test/jalview/gui/SequenceRendererTest.java
+++ b/test/jalview/gui/SequenceRendererTest.java
@@ -22,6 +22,7 @@ package jalview.gui;
 
 import static org.testng.Assert.assertEquals;
 
+import jalview.api.AlignViewportI;
 import jalview.bin.Jalview;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
@@ -41,7 +42,7 @@ import org.testng.annotations.Test;
 public class SequenceRendererTest
 {
   AlignmentI al;
-  AlignViewport av;
+  AlignViewportI av;
 
   SequenceI seq1;
 
diff --git a/test/jalview/hmmer/HMMERTest.java b/test/jalview/hmmer/HMMERTest.java
new file mode 100644
index 0000000..8f96d04
--- /dev/null
+++ b/test/jalview/hmmer/HMMERTest.java
@@ -0,0 +1,132 @@
+package jalview.hmmer;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertTrue;
+import static org.testng.Assert.fail;
+
+import jalview.bin.Jalview;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenMarkovModel;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.io.HMMFile;
+import jalview.util.MessageManager;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.simple.Option;
+
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.util.ArrayList;
+
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+public class HMMERTest {
+
+  AlignFrame frame;
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpBeforeClass() throws Exception
+  {
+    /*
+     * NB: check HMMER_PATH in testProps.jvprops is valid for
+     * the machine on which this runs
+     */
+    Jalview.main(
+            new String[]
+    { "-noquestionnaire", "-nonews", "-props",
+                "test/jalview/hmmer/testProps.jvprops", "-open",
+                "examples/uniref50.fa" });
+    frame = Desktop.getAlignFrames()[0];
+  }
+
+  @AfterClass(alwaysRun = true)
+  public static void tearDownAfterClass() throws Exception
+  {
+    Desktop.instance.closeAll_actionPerformed(null);
+  }
+
+  /**
+   * Test with a dependency on locally installed hmmbuild binaries
+   * 
+   * @throws MalformedURLException
+   * @throws IOException
+   */
+  @Test(groups = "External")
+  public void testHMMBuildThenHMMAlign()
+          throws MalformedURLException, IOException
+  {
+    /*
+     * run hmmbuild - note the side-effect of selecting the HMM
+     * sequence that gets added to the alignment
+     */
+    testHMMBuild();
+    HiddenMarkovModel hmm = frame.getSelectedHMM();
+    assertNotNull(hmm);
+
+    /*
+     * now run hmmalign - with respect to the select HMM profile
+     */
+    testHMMAlign();
+  }
+
+  public void testHMMBuild()
+  {
+    /*
+     * set up argument to run hmmbuild for the alignment
+     */
+    ArrayList<ArgumentI> params = new ArrayList<>();
+    String argName = MessageManager.getString("label.hmmbuild_for");
+    String argValue = MessageManager.getString("label.alignment");
+    params.add(
+            new Option(argName, null, false, null, argValue, null, null));
+
+    HMMBuild builder = new HMMBuild(frame, params);
+    builder.run();
+
+    SequenceI seq = frame.getViewport().getAlignment().getSequenceAt(0);
+    HiddenMarkovModel hmm = seq.getHMM();
+    assertNotNull(hmm);
+
+    assertEquals(hmm.getLength(), 148);
+    assertEquals(hmm.getAlphabetType(), "amino");
+    assertEquals(hmm.getName(), "Alignment_HMM");
+    assertEquals(hmm.getProperty(HMMFile.EFF_NUMBER_OF_SEQUENCES),
+            "0.648193");
+  }
+
+  public void testHMMAlign()
+  {
+    HMMAlign thread = new HMMAlign(frame,
+            new ArrayList<ArgumentI>());
+    thread.run();
+
+    AlignFrame[] alignFrames = Desktop.getAlignFrames();
+    if (alignFrames == null)
+    {
+      fail("No align frame loaded");
+    }
+
+    /*
+     * now have the original align frame, and another for realigned sequences
+     */
+    assertEquals(alignFrames.length, 2);
+    AlignmentI original = alignFrames[0].getViewport().getAlignment();
+    assertNotNull(original);
+    AlignmentI realigned = alignFrames[1].getViewport().getAlignment();
+    assertNotNull(realigned);
+    assertNotNull(original.getHmmConsensus());
+    assertNotNull(realigned.getHmmConsensus());
+
+    SequenceI ferCapan = original.findName("FER_CAPAN");
+    assertTrue(ferCapan.getSequenceAsString().startsWith("MA------SVSAT"));
+
+    SequenceI ferCapanRealigned = realigned.findName("FER_CAPAN");
+    assertTrue(ferCapanRealigned.getSequenceAsString()
+            .startsWith("-------m-A----SVSAT"));
+  }
+}
+
diff --git a/test/jalview/hmmer/testProps.jvprops b/test/jalview/hmmer/testProps.jvprops
new file mode 100644
index 0000000..05cd493
--- /dev/null
+++ b/test/jalview/hmmer/testProps.jvprops
@@ -0,0 +1,88 @@
+#---JalviewX Properties File---
+#Fri Apr 25 09:54:25 BST 2014
+SCREEN_Y=768
+SCREEN_X=936
+SHOW_WSDISCOVERY_ERRORS=true
+LATEST_VERSION=2.8.0b1
+SHOW_CONSERVATION=true
+JALVIEW_RSS_WINDOW_SCREEN_WIDTH=550
+JAVA_CONSOLE_SCREEN_WIDTH=450
+LAST_DIRECTORY=/Volumes/Data/Users/jimp/Documents/testing/Jalview/examples
+ID_ITALICS=true
+SORT_ALIGNMENT=No sort
+SHOW_IDENTITY=true
+WSMENU_BYHOST=false
+SEQUENCE_LINKS=EMBL-EBI Search|http\://www.ebi.ac.uk/ebisearch/search.ebi?db\=allebi&query\=$SEQUENCE_ID$
+SHOW_FULLSCREEN=false
+RECENT_URL=http\://www.jalview.org/examples/exampleFile_2_7.jar
+FONT_NAME=SansSerif
+BLC_JVSUFFIX=true
+VERSION_CHECK=false
+YEAR=2011
+SHOW_DBREFS_TOOLTIP=true
+MSF_JVSUFFIX=true
+SCREENGEOMETRY_HEIGHT=1600
+JAVA_CONSOLE_SCREEN_Y=475
+JAVA_CONSOLE_SCREEN_X=830
+PFAM_JVSUFFIX=true
+PIR_JVSUFFIX=true
+STARTUP_FILE=http\://www.jalview.org/examples/exampleFile_2_3.jar
+JAVA_CONSOLE_SCREEN_HEIGHT=162
+PIR_MODELLER=false
+GAP_SYMBOL=-
+SHOW_QUALITY=true
+SHOW_OCCUPANCY=true
+SHOW_GROUP_CONSERVATION=false
+SHOW_JWS2_SERVICES=true
+SHOW_NPFEATS_TOOLTIP=true
+FONT_STYLE=plain
+ANTI_ALIAS=false
+SORT_BY_TREE=false
+RSBS_SERVICES=|Multi-Harmony|Analysis|Sequence Harmony and Multi-Relief (Brandt et al. 2010)|hseparable,gapCharacter\='-',returns\='ANNOTATION'|?tool\=jalview|http\://zeus.few.vu.nl/programs/shmrwww/index.php?tool\=jalview&groups\=$PARTITION\:min\='2',minsize\='2',sep\=' '$&ali_file\=$ALIGNMENT\:format\='FASTA',writeasfile$
+AUTHORFNAMES=Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui, Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton
+JALVIEW_RSS_WINDOW_SCREEN_HEIGHT=328
+SHOW_GROUP_CONSENSUS=false
+SHOW_CONSENSUS_HISTOGRAM=true
+SHOW_OVERVIEW=false
+AUTHORS=J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+FIGURE_AUTOIDWIDTH=false
+SCREEN_WIDTH=900
+ANNOTATIONCOLOUR_MIN=ffc800
+SHOW_STARTUP_FILE=false
+RECENT_FILE=examples/uniref50.fa\t/Volumes/Data/Users/jimp/Documents/testing/Jalview/examples/RF00031_folded.stk\t/Volumes/Data/Users/jimp/bs_ig_mult.out
+DEFAULT_FILE_FORMAT=FASTA
+SHOW_JAVA_CONSOLE=false
+VERSION=2.8b1
+FIGURE_USERIDWIDTH=
+WSMENU_BYTYPE=false
+DEFAULT_COLOUR=None
+NOQUESTIONNAIRES=true
+JALVIEW_NEWS_RSS_LASTMODIFIED=Apr 23, 2014 2\:53\:26 PM
+BUILD_DATE=01 November 2013
+PILEUP_JVSUFFIX=true
+SHOW_CONSENSUS_LOGO=false
+SCREENGEOMETRY_WIDTH=2560
+SHOW_ANNOTATIONS=true
+JALVIEW_RSS_WINDOW_SCREEN_Y=0
+USAGESTATS=false
+JALVIEW_RSS_WINDOW_SCREEN_X=0
+SHOW_UNCONSERVED=false
+SHOW_JVSUFFIX=true
+DAS_LOCAL_SOURCE=
+SCREEN_HEIGHT=650
+ANNOTATIONCOLOUR_MAX=ff0000
+AUTO_CALC_CONSENSUS=true
+FASTA_JVSUFFIX=true
+DAS_ACTIVE_SOURCE=uniprot\t
+JWS2HOSTURLS=http\://www.compbio.dundee.ac.uk/jabaws
+PAD_GAPS=false
+CLUSTAL_JVSUFFIX=true
+SHOW_ENFIN_SERVICES=true
+FONT_SIZE=10
+RIGHT_ALIGN_IDS=false
+USE_PROXY=false
+WRAP_ALIGNMENT=false
+#DAS_REGISTRY_URL=http\://www.dasregistry.org/das/ # retired 01/05/2015
+DAS_REGISTRY_URL=http\://www.ebi.ac.uk/das-srv/registry/das/
+logs.Jalview.level=DEBUG
+HMMER_PATH=/Users/gmcarstairs/software/hmmer-3.1b2-macosx-intel/binaries
diff --git a/test/jalview/io/AnnotatedPDBFileInputTest.java b/test/jalview/io/AnnotatedPDBFileInputTest.java
index e14a478..c0038a1 100644
--- a/test/jalview/io/AnnotatedPDBFileInputTest.java
+++ b/test/jalview/io/AnnotatedPDBFileInputTest.java
@@ -39,6 +39,7 @@ import jalview.structure.StructureImportSettings.StructureParser;
 import java.io.File;
 import java.util.List;
 
+import org.junit.Assert;
 import org.testng.annotations.AfterClass;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
@@ -101,18 +102,19 @@ public class AnnotatedPDBFileInputTest
     }
   }
 
-  @Test(groups = { "Functional" })
+  @Test(groups = { "Functional" }, enabled = false)
   public void checkPDBannotationSource()
   {
-
+    Assert.fail(
+            "This test is incorrect - does not verify that JmolParser's annotation rows can be recognised as generated by the Jmol parser.");
     for (SequenceI asq : al.getSequences())
     {
       for (AlignmentAnnotation aa : asq.getAnnotation())
       {
 
         System.out.println("CalcId: " + aa.getCalcId());
-        if (StructureImportSettings.getDefaultPDBFileParser().equals(
-                StructureParser.JALVIEW_PARSER))
+        if (StructureImportSettings.getDefaultPDBFileParser()
+                .equals(StructureParser.JALVIEW_PARSER))
         {
           assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
         }
diff --git a/test/jalview/io/CrossRef2xmlTests.java b/test/jalview/io/CrossRef2xmlTests.java
index b3db4de..2b8a62f 100644
--- a/test/jalview/io/CrossRef2xmlTests.java
+++ b/test/jalview/io/CrossRef2xmlTests.java
@@ -45,6 +45,7 @@ import junit.extensions.PA;
 
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
+import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
 @Test(singleThreaded = true)
@@ -59,6 +60,14 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
   }
 
+  @DataProvider(name = "initialAccessions")
+  static Object[][] getAccessions()
+  {
+    return new String[][] { { "UNIPROT", "P00338" },
+        { "UNIPROT", "Q8Z9G6" },
+        { "ENSEMBLGENOMES", "CAD01290" } };
+  }
+
   /**
    * test store and recovery of all reachable cross refs from all reachable
    * crossrefs for one or more fetched db refs. Currently, this test has a known
@@ -66,8 +75,13 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
    * 
    * @throws Exception
    */
-  @Test(groups = { "Operational" }, enabled = true)
-  public void testRetrieveAndShowCrossref() throws Exception
+  @Test(
+    groups =
+    { "Operational" },
+    dataProvider = "initialAccessions",
+    enabled = true)
+  public void testRetrieveAndShowCrossref(String forSource,
+          String forAccession) throws Exception
   {
 
     List<String> failedDBRetr = new ArrayList<>();
@@ -97,8 +111,8 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
     List<String> keyseq = new ArrayList<>();
     Map<String, File> savedProjects = new HashMap<>();
 
-    for (String[] did : new String[][] { { "UNIPROT", "P00338" } })
-    {
+//    for (String[] did : new String[][] { { "UNIPROT", "P00338" } })
+//    {
       // pass counters - 0 - first pass, 1 means retrieve project rather than
       // perform action
       int pass1 = 0, pass2 = 0, pass3 = 0;
@@ -108,7 +122,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
       // { pass 2 = 0 { pass 3 = 0 } }
       do
       {
-        String first = did[0] + " " + did[1];
+        String first = forSource + " " + forAccession;//did[0] + " " + did[1];
         AlignFrame af = null;
         boolean dna;
         AlignmentI retral;
@@ -120,7 +134,8 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
           // retrieve dbref
 
           List<AlignFrame> afs = jalview.gui.SequenceFetcher.fetchAndShow(
-                  did[0], did[1]);
+                forSource, forAccession);
+        // did[0], did[1]);
           if (afs.size() == 0)
           {
             failedDBRetr.add("Didn't retrieve " + first);
@@ -416,7 +431,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
           pass1++;
         }
       } while (pass1 < 3);
-    }
+
     if (failedXrefMenuItems.size() > 0)
     {
       for (String s : failedXrefMenuItems)
diff --git a/test/jalview/io/FileFormatsTest.java b/test/jalview/io/FileFormatsTest.java
index 7810504..724bae0 100644
--- a/test/jalview/io/FileFormatsTest.java
+++ b/test/jalview/io/FileFormatsTest.java
@@ -55,7 +55,7 @@ public class FileFormatsTest
   @Test(groups = "Functional")
   public void testGetReadableFormats()
   {
-    String expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview]";
+    String expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview, HMMER3]";
     FileFormats formats = FileFormats.getInstance();
     assertEquals(formats.getReadableFormats().toString(), expected);
   }
@@ -63,25 +63,25 @@ public class FileFormatsTest
   @Test(groups = "Functional")
   public void testGetWritableFormats()
   {
-    String expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP]";
+    String expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, HMMER3]";
     FileFormats formats = FileFormats.getInstance();
     assertEquals(formats.getWritableFormats(true).toString(), expected);
-    expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, Jalview]";
+    expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, Jalview, HMMER3]";
     assertEquals(formats.getWritableFormats(false).toString(), expected);
   }
 
   @Test(groups = "Functional")
   public void testDeregisterFileFormat()
   {
-    String writable = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP]";
-    String readable = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview]";
+    String writable = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, HMMER3]";
+    String readable = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview, HMMER3]";
     FileFormats formats = FileFormats.getInstance();
     assertEquals(formats.getWritableFormats(true).toString(), writable);
     assertEquals(formats.getReadableFormats().toString(), readable);
 
     formats.deregisterFileFormat(FileFormat.Fasta.getName());
-    writable = "[PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP]";
-    readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview]";
+    writable = "[PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, HMMER3]";
+    readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview, HMMER3]";
     assertEquals(formats.getWritableFormats(true).toString(), writable);
     assertEquals(formats.getReadableFormats().toString(), readable);
 
@@ -89,8 +89,8 @@ public class FileFormatsTest
      * re-register the format: it gets added to the end of the list
      */
     formats.registerFileFormat(FileFormat.Fasta);
-    writable = "[PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, Fasta]";
-    readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview, Fasta]";
+    writable = "[PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, HMMER3, Fasta]";
+    readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview, HMMER3, Fasta]";
     assertEquals(formats.getWritableFormats(true).toString(), writable);
     assertEquals(formats.getReadableFormats().toString(), readable);
   }
diff --git a/test/jalview/io/FormatAdapterTest.java b/test/jalview/io/FormatAdapterTest.java
index b500266..3812a09 100644
--- a/test/jalview/io/FormatAdapterTest.java
+++ b/test/jalview/io/FormatAdapterTest.java
@@ -56,8 +56,17 @@ public class FormatAdapterTest
   {
     try
     {
-      AlignmentI al = new FormatAdapter().readFile("examples/uniref50.fa",
+      AlignmentI al;
+      if (format == FileFormat.HMMER3)
+      {
+        al = new FormatAdapter().readFile("examples/uniref50.hmm",
+                DataSourceType.FILE, FileFormat.HMMER3);
+      }
+      else
+      {
+        al = new FormatAdapter().readFile("examples/uniref50.fa",
               DataSourceType.FILE, FileFormat.Fasta);
+      }
 
       /*
        * 'gap' is the gap character used in the alignment data file here,
@@ -73,8 +82,9 @@ public class FormatAdapterTest
       AlignmentI reloaded = new FormatAdapter().readFile(formatted,
               DataSourceType.PASTE, format);
       List<SequenceI> reread = reloaded.getSequences();
-      assertEquals("Wrong number of reloaded sequences", seqs.length,
-              reread.size());
+        assertEquals("Wrong number of reloaded sequences", seqs.length,
+                reread.size());
+
 
       int i = 0;
       for (SequenceI seq : reread)
@@ -131,7 +141,7 @@ public class FormatAdapterTest
   @DataProvider(name = "formats")
   static Object[][] getFormats()
   {
-    List<FileFormatI> both = new ArrayList<FileFormatI>();
+    List<FileFormatI> both = new ArrayList<>();
     for (FileFormatI format : FileFormats.getInstance().getFormats())
     {
       if (format.isReadable() && format.isWritable()
diff --git a/test/jalview/io/HMMFileTest.java b/test/jalview/io/HMMFileTest.java
new file mode 100644
index 0000000..cf74f55
--- /dev/null
+++ b/test/jalview/io/HMMFileTest.java
@@ -0,0 +1,531 @@
+package jalview.io;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertNull;
+import static org.testng.Assert.assertTrue;
+
+import jalview.datamodel.HMMNode;
+import jalview.datamodel.HiddenMarkovModel;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Scanner;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+import junit.extensions.PA;
+
+public class HMMFileTest {
+
+  HMMFile fn3;
+
+  HMMFile pKinase;
+
+  HMMFile made1;
+
+  @BeforeClass(alwaysRun = true)
+  public void setUp() throws IOException
+  {
+    fn3 = new HMMFile("test/jalview/io/test_fn3_hmm.txt",
+            DataSourceType.FILE);
+
+    pKinase = new HMMFile("test/jalview/io/test_PKinase_hmm.txt",
+            DataSourceType.FILE);
+
+    made1 = new HMMFile("test/jalview/io/test_MADE1_hmm.txt",
+            DataSourceType.FILE);
+  }
+
+  @Test(groups = "Functional")
+  public void testParse() throws IOException
+  {
+    HiddenMarkovModel hmm = pKinase.getHMM();
+    assertEquals(hmm.getName(), "Pkinase");
+    assertEquals(hmm.getProperty(HMMFile.ACCESSION_NUMBER), "PF00069.17");
+    assertEquals(hmm.getProperty(HMMFile.DESCRIPTION),
+            "Protein kinase domain");
+    assertEquals(hmm.getLength(), 260);
+    assertNull(hmm.getProperty(HMMFile.MAX_LENGTH));
+    assertEquals(hmm.getAlphabetType(), "amino");
+    assertFalse(hmm.getBooleanProperty(HMMFile.REFERENCE_ANNOTATION));
+    assertFalse(hmm.getBooleanProperty(HMMFile.MASKED_VALUE));
+    assertTrue(hmm.getBooleanProperty(HMMFile.CONSENSUS_RESIDUE));
+    assertTrue(hmm.getBooleanProperty(HMMFile.CONSENSUS_STRUCTURE));
+    assertTrue(hmm.getBooleanProperty(HMMFile.MAP));
+    assertEquals(hmm.getProperty(HMMFile.DATE), "Thu Jun 16 11:44:06 2011");
+    assertNull(hmm.getProperty(HMMFile.COMMAND_LOG));
+    assertEquals(hmm.getProperty(HMMFile.NUMBER_OF_SEQUENCES), "54");
+    assertEquals(hmm.getProperty(HMMFile.EFF_NUMBER_OF_SEQUENCES),
+            "3.358521");
+    assertEquals(hmm.getProperty(HMMFile.CHECK_SUM), "3106786190");
+    assertEquals(hmm.getProperty(HMMFile.GATHERING_THRESHOLD),
+            "70.30 70.30");
+    assertEquals(hmm.getProperty(HMMFile.TRUSTED_CUTOFF), "70.30 70.30");
+    assertEquals(hmm.getProperty(HMMFile.NOISE_CUTOFF), "70.20 70.20");
+  
+    assertEquals(hmm.getSymbols(), "ACDEFGHIKLMNPQRSTVWY");
+  
+    assertEquals(hmm.getMatchEmissionProbability(0, 'Y'), 0.16102, 0.001d);
+    assertEquals(hmm.getMatchEmissionProbability(11, 'P'), 0.0130, 0.001d);
+    assertEquals(hmm.getMatchEmissionProbability(24, 'I'), 0.02583, 0.001d);
+    assertEquals(hmm.getMatchEmissionProbability(83, 'C'), 0.008549,
+            0.001d);
+    assertEquals(hmm.getMatchEmissionProbability(332, 'E'), 0.07998,
+            0.001d);
+    assertEquals(hmm.getMatchEmissionProbability(381, 'D'), 0.014465,
+            0.001d);
+    assertEquals(hmm.getMatchEmissionProbability(475, 'Y'), 0.02213,
+            0.001d);
+  
+    assertEquals(hmm.getInsertEmissionProbability(1, 'C'), 0.012, 0.001d);
+    assertEquals(hmm.getInsertEmissionProbability(14, 'H'), 0.02411,
+            0.001d);
+    assertEquals(hmm.getInsertEmissionProbability(23, 'L'), 0.06764,
+            0.001d);
+    assertEquals(hmm.getInsertEmissionProbability(90, 'D'), 0.0623, 0.001d);
+    assertEquals(hmm.getInsertEmissionProbability(374, 'T'), 0.0623,
+            0.001d);
+    assertEquals(hmm.getInsertEmissionProbability(470, 'P'), 0.0647,
+            0.001d);
+  
+    assertEquals(hmm.getStateTransitionProbability(2, 6), 0.3848, 0.001d);
+    assertEquals(hmm.getStateTransitionProbability(38, 3), 0.5382, 0.001d);
+    assertEquals(hmm.getStateTransitionProbability(305, 3), 0.2916, 0.001d);
+    assertEquals(hmm.getStateTransitionProbability(380, 0), 0.99, 0.001d);
+    assertEquals(hmm.getStateTransitionProbability(453, 1), 0.0066, 0.001d);
+  
+    assertEquals(hmm.getNodeMapPosition(3), 3);
+    assertEquals(hmm.getReferenceAnnotation(7), '-');
+    assertEquals(hmm.getConsensusResidue(23), 't');
+    assertEquals(hmm.getMaskedValue(30), '-');
+    assertEquals(hmm.getConsensusStructure(56), 'S');
+  
+    assertEquals(hmm.getNodeMapPosition(78), 136);
+    assertEquals(hmm.getReferenceAnnotation(93), '-');
+    assertEquals(hmm.getConsensusResidue(145), 'a');
+    assertEquals(hmm.getMaskedValue(183), '-');
+    assertEquals(hmm.getConsensusStructure(240), 'H');
+  }
+
+  /**
+   * Test that Jalview can parse an HMM file even with a bunch of 'mandatory'
+   * fields missing (including no MAP annotation or // terminator line)
+   * 
+   * @throws IOException
+   */
+  @Test(groups = "Functional")
+  public void testParse_minimalFile() throws IOException
+  {
+    /*
+     * ALPH is absent, alphabet inferred from HMM header line
+     * Optional COMPO line is absent
+     * first line after HMM is a guide line for readability
+     * next line is BEGIN node insert emissions
+     * next line is BEGIN node transitions
+     * next line is first sequence node match emissions 1.1 1.2 1.3
+     * next line is first sequence node insert emissions 1.4 1.5 1.6
+     * last line is first sequence node transitions
+     */
+    //@formatter:off
+    String hmmData = 
+            "HMMER3\n" +
+            "HMM P M J\n" +
+            // both spec and parser require a line after the HMM line
+            " m->m m->i m->d i->m i->i d->m d->d\n" +
+            " 0.1 0.2 0.3\n" + 
+            " 0.4 0.5 0.6 0.7 0.8 0.9 0.95\n" + 
+            " 1 1.1 1.2 1.3 - - - - -\n" + 
+            " 1.4 1.5 1.6\n" + 
+            " 1.7 1.8 1.9 2.0 2.1 2.2 2.3\n" +
+            " 2 1.01 1.02 1.03 - - - - -\n" + 
+            " 1.04 1.05 1.06\n" + 
+            " 1.7 1.8 1.9 2.0 2.1 2.2 2.3\n";
+    //@formatter:on
+    HMMFile parser = new HMMFile(hmmData, DataSourceType.PASTE);
+    HiddenMarkovModel hmm = parser.getHMM();
+    assertNotNull(hmm);
+    assertEquals(hmm.getSymbols(), "PMJ");
+    // no LENG property: this should return node count excluding BEGIN node
+    assertEquals(hmm.getLength(), 2);
+
+    // node 1 (implicitly mapped to column 0)
+    double prob = hmm.getMatchEmissionProbability(0, 'p');
+    assertEquals(prob, Math.pow(Math.E, -1.1));
+    prob = hmm.getInsertEmissionProbability(0, 'J');
+    assertEquals(prob, Math.pow(Math.E, -1.6));
+
+    // node 2 (implicitly mapped to column 1)
+    prob = hmm.getMatchEmissionProbability(1, 'M');
+    assertEquals(prob, Math.pow(Math.E, -1.02));
+    prob = hmm.getInsertEmissionProbability(1, 'm');
+    assertEquals(prob, Math.pow(Math.E, -1.05));
+  }
+  
+  @Test(groups = "Functional")
+  public void testParseHeaderLines_amino() throws IOException
+  {
+    FileReader fr = new FileReader(
+            new File("test/jalview/io/test_fn3_hmm.txt"));
+    BufferedReader br = new BufferedReader(fr);
+    HiddenMarkovModel hmm = new HiddenMarkovModel();
+    HMMFile testee = new HMMFile();
+    PA.setValue(testee, "hmm", hmm);
+    testee.parseHeaderLines(br);
+    br.close();
+    fr.close();
+  
+    assertEquals(hmm.getName(), "fn3");
+    assertEquals(hmm.getProperty(HMMFile.ACCESSION_NUMBER), "PF00041.13");
+    assertEquals(hmm.getProperty(HMMFile.DESCRIPTION),
+            "Fibronectin type III domain");
+    assertEquals(hmm.getProperty(HMMFile.LENGTH), "86");
+    assertNull(hmm.getProperty(HMMFile.MAX_LENGTH));
+    assertEquals(hmm.getAlphabetType(), "amino");
+    assertFalse(hmm.getBooleanProperty(HMMFile.REFERENCE_ANNOTATION));
+    assertFalse(hmm.getBooleanProperty(HMMFile.MASKED_VALUE));
+    assertTrue(hmm.getBooleanProperty(HMMFile.CONSENSUS_RESIDUE));
+    assertTrue(hmm.getBooleanProperty(HMMFile.CONSENSUS_STRUCTURE));
+
+    assertTrue(hmm.getBooleanProperty(HMMFile.MAP));
+    assertEquals(hmm.getProperty(HMMFile.DATE), "Fri Jun 20 08:22:31 2014");
+    assertNull(hmm.getProperty(HMMFile.COMMAND_LOG));
+    assertEquals(hmm.getProperty(HMMFile.NUMBER_OF_SEQUENCES), "106");
+    assertEquals(hmm.getProperty(HMMFile.EFF_NUMBER_OF_SEQUENCES),
+            "11.415833");
+    assertEquals(hmm.getProperty(HMMFile.CHECK_SUM), "3564431818");
+    assertEquals(hmm.getProperty(HMMFile.GATHERING_THRESHOLD), "8.00 7.20");
+    assertEquals(hmm.getProperty(HMMFile.TRUSTED_CUTOFF), "8.00 7.20");
+    assertEquals(hmm.getProperty(HMMFile.NOISE_CUTOFF), "7.90 7.90");
+    assertEquals(hmm.getViterbi(), "-9.7737  0.71847");
+    assertEquals(hmm.getMSV(), "-9.4043  0.71847");
+    assertEquals(hmm.getForward(), "-3.8341  0.71847");
+  }
+  
+  @Test(groups = "Functional")
+  public void testParseHeaderLines_dna() throws IOException
+  {
+    FileReader fr = new FileReader(
+            new File("test/jalview/io/test_MADE1_hmm.txt"));
+    BufferedReader br = new BufferedReader(fr);
+    HiddenMarkovModel hmm = new HiddenMarkovModel();
+    HMMFile testee = new HMMFile();
+    PA.setValue(testee, "hmm", hmm);
+    testee.parseHeaderLines(br);
+    br.close();
+    fr.close();
+  
+    assertEquals(hmm.getName(), "MADE1");
+    assertEquals(hmm.getProperty(HMMFile.ACCESSION_NUMBER),
+            "DF0000629.2");
+    assertEquals(hmm.getProperty(HMMFile.DESCRIPTION),
+            "MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon");
+    assertEquals(hmm.getProperty(HMMFile.LENGTH), "80");
+    assertEquals(hmm.getProperty(HMMFile.MAX_LENGTH), "426");
+    assertEquals(hmm.getAlphabetType(), "DNA");
+    assertTrue(hmm.getBooleanProperty(HMMFile.REFERENCE_ANNOTATION));
+    assertFalse(hmm.getBooleanProperty(HMMFile.MASKED_VALUE));
+    assertTrue(hmm.getBooleanProperty(HMMFile.CONSENSUS_RESIDUE));
+    assertFalse(hmm.getBooleanProperty(HMMFile.CONSENSUS_STRUCTURE));
+    assertTrue(hmm.getBooleanProperty(HMMFile.MAP));
+    assertEquals(hmm.getProperty(HMMFile.DATE), "Tue Feb 19 20:33:41 2013");
+    assertNull(hmm.getProperty(HMMFile.COMMAND_LOG));
+    assertEquals(hmm.getProperty(HMMFile.NUMBER_OF_SEQUENCES), "1997");
+    assertEquals(hmm.getProperty(HMMFile.EFF_NUMBER_OF_SEQUENCES), "3.911818");
+    assertEquals(hmm.getProperty(HMMFile.CHECK_SUM), "3015610723");
+    assertEquals(hmm.getProperty(HMMFile.GATHERING_THRESHOLD),
+            "2.324 4.234");
+    assertEquals(hmm.getProperty(HMMFile.TRUSTED_CUTOFF), "2.343 1.212");
+    assertEquals(hmm.getProperty(HMMFile.NOISE_CUTOFF), "2.354 5.456");
+    assertEquals(hmm.getViterbi(), "-9.3632  0.71858");
+    assertEquals(hmm.getMSV(), "-8.5786  0.71858");
+    assertEquals(hmm.getForward(), "-3.4823  0.71858");
+  }
+  
+  @Test(groups = "Functional")
+  public void testFillList() throws IOException
+  {
+    Scanner scanner1 = new Scanner("1.3 2.4 5.3 3.9 9.8 4.7 4.3 2.3 6.9");
+    ArrayList<Double> filledArray = new ArrayList<>();
+  
+    filledArray.add(0.27253);
+    filledArray.add(0.0907);
+    filledArray.add(0.00499);
+    filledArray.add(0.02024);
+    filledArray.add(0.00005);
+    filledArray.add(0.00909);
+    filledArray.add(0.01357);
+    filledArray.add(0.10026);
+    filledArray.add(0.001);
+  
+    double[] testList = HMMFile.parseDoubles(scanner1, 9);
+
+    for (int i = 0; i < 9; i++)
+    {
+      assertEquals(testList[i], filledArray.get(i), 0.001d);
+    }
+
+    filledArray.clear();
+    scanner1.close();
+  
+    Scanner scanner2 = new Scanner(
+            "1.346 5.554 35.345 5.64 1.4");
+    filledArray.add(0.2603);
+    filledArray.add(0.00387);
+    filledArray.add(0d);
+    filledArray.add(0.00355);
+    filledArray.add(0.2466);
+  
+    testList = HMMFile.parseDoubles(scanner2, 5);
+
+    for (int i = 0; i < 5; i++)
+    {
+      assertEquals(testList[i], filledArray.get(i), 0.001d);
+    }
+  }
+  
+  @Test(groups = "Functional")
+  public void testParseModel() throws IOException
+  {
+    FileReader fr = new FileReader(
+            new File("test/jalview/io/test_MADE1_hmm.txt"));
+    BufferedReader br = new BufferedReader(fr);
+    HiddenMarkovModel testHMM = new HiddenMarkovModel();
+    String line = null;
+    do
+    {
+      line = br.readLine(); // skip header lines up to HMM plus one
+    } while (!line.startsWith("HMM "));
+    br.readLine();
+
+    made1.parseModel(br);
+    testHMM = made1.getHMM();
+
+    br.close();
+    fr.close();
+  
+    assertEquals(testHMM.getMatchEmissionProbability(1, 'C'), 0.09267,
+            0.001d);
+    assertEquals(testHMM.getMatchEmissionProbability(25, 'G'), 0.07327,
+            0.001d);
+    assertEquals(testHMM.getMatchEmissionProbability(1092, 'C'), 0.04184,
+            0.001d);
+    assertEquals(testHMM.getMatchEmissionProbability(1107, 'G'), 0.07,
+            0.001d);
+  
+    assertEquals(testHMM.getInsertEmissionProbability(0, 'G'), 0.25,
+            0.001d);
+    assertEquals(testHMM.getInsertEmissionProbability(247, 'T'), 0.2776,
+            0.001d);
+    assertEquals(testHMM.getInsertEmissionProbability(1096, 'T'), 0.25,
+            0.001d);
+    assertEquals(testHMM.getInsertEmissionProbability(1111, 'T'), 0.25,
+            0.001d);
+
+    assertEquals(testHMM.getStateTransitionProbability(1, 0), 0.9634,
+            0.001d);
+    assertEquals(testHMM.getStateTransitionProbability(5, 1), 0.0203,
+            0.001d);
+    assertEquals(testHMM.getStateTransitionProbability(14, 3), 0.2515,
+            0.001d);
+    assertEquals(testHMM.getStateTransitionProbability(65, 4), 0.78808,
+            0.001d);
+    assertEquals(testHMM.getStateTransitionProbability(1080, 2), 0.01845,
+            0.001d);
+    assertEquals(testHMM.getStateTransitionProbability(1111, 6),
+            Double.NEGATIVE_INFINITY);
+  }
+  
+  @Test(groups = "Functional")
+  public void testParseAnnotations()
+  {
+    HMMFile testFile = new HMMFile();
+    HiddenMarkovModel hmm = new HiddenMarkovModel();
+    PA.setValue(testFile, "hmm", hmm);
+
+    List<HMMNode> nodes = new ArrayList<>();
+    nodes.add(new HMMNode()); // BEGIN node
+  
+    hmm.setProperty(HMMFile.CONSENSUS_RESIDUE, "yes");
+    hmm.setProperty(HMMFile.MAP, "yes");
+    hmm.setProperty(HMMFile.REFERENCE_ANNOTATION, "yes");
+    hmm.setProperty(HMMFile.CONSENSUS_STRUCTURE, "yes");
+    hmm.setProperty(HMMFile.MASKED_VALUE, "yes");
+    Scanner scanner = new Scanner("1345 t t t t");
+    HMMNode node = new HMMNode();
+    nodes.add(node);
+    testFile.parseAnnotations(scanner, node);
+  
+    hmm.setProperty(HMMFile.CONSENSUS_RESIDUE, "yes");
+    hmm.setProperty(HMMFile.MAP, "no");
+    hmm.setProperty(HMMFile.REFERENCE_ANNOTATION, "yes");
+    hmm.setProperty(HMMFile.CONSENSUS_STRUCTURE, "no");
+    hmm.setProperty(HMMFile.MASKED_VALUE, "no");
+    Scanner scanner2 = new Scanner("- y x - -");
+    node = new HMMNode();
+    nodes.add(node);
+    testFile.parseAnnotations(scanner2, node);
+
+    hmm.setNodes(nodes);
+
+    assertEquals(hmm.getNodeMapPosition(1), 1345);
+    assertEquals(hmm.getConsensusResidue(1), 't');
+    assertEquals(hmm.getReferenceAnnotation(1), 't');
+    assertEquals(hmm.getMaskedValue(1), 't');
+    assertEquals(hmm.getConsensusStructure(1), 't');
+  
+    scanner.close();
+  }
+  
+  /**
+   * tests to see if file produced by the output matches the file from the input
+   * 
+   * @throws IOException
+   */
+  @Test(groups = "Functional")
+  public void testPrint_roundTrip() throws IOException
+  {
+    String output = pKinase.print();
+    HMMFile pKinaseClone = new HMMFile(
+            new FileParse(output, DataSourceType.PASTE));
+    HiddenMarkovModel pKinaseHMM = pKinase.getHMM();
+    HiddenMarkovModel pKinaseCloneHMM = pKinaseClone.getHMM();
+  
+    checkModelsMatch(pKinaseHMM, pKinaseCloneHMM);
+  }
+
+  /**
+   * A helper method to check two HMM models have the same values
+   * 
+   * @param model1
+   * @param model2
+   */
+  protected void checkModelsMatch(HiddenMarkovModel model1,
+          HiddenMarkovModel model2)
+  {
+    assertEquals(model1.getLength(), model2.getLength());
+
+    for (int i = 0; i < model1.getLength(); i++)
+    {
+      String msg = "For Node" + i;
+      assertEquals(model1.getNode(i).getMatchEmissions(),
+              model2.getNode(i).getMatchEmissions(), msg);
+      assertEquals(model1.getNode(i).getInsertEmissions(),
+              model2.getNode(i).getInsertEmissions(), msg);
+      assertEquals(model1.getNode(i).getStateTransitions(),
+              model2.getNode(i).getStateTransitions(), msg);
+  
+      if (i > 0)
+      {
+        assertEquals(model1.getNodeMapPosition(i),
+                model2.getNodeMapPosition(i), msg);
+        assertEquals(model1.getReferenceAnnotation(i),
+                model2.getReferenceAnnotation(i), msg);
+        assertEquals(model1.getConsensusResidue(i),
+                model2.getConsensusResidue(i), msg);
+      }
+    }
+  }
+  
+  @Test(groups = "Functional")
+  public void testAppendProperties() throws FileNotFoundException
+  {
+    StringBuilder sb = new StringBuilder();
+    fn3.appendProperties(sb);
+
+    Scanner testScanner = new Scanner(sb.toString());
+  
+    String[] expected = new String[] { "HMMER3/f [3.1b1 | May 2013]",
+        "NAME  fn3", "ACC   PF00041.13",
+        "DESC  Fibronectin type III domain", "LENG  86", "ALPH  amino",
+        "RF    no", "MM    no", "CONS  yes", "CS    yes", "MAP   yes",
+        "DATE  Fri Jun 20 08:22:31 2014", "NSEQ  106", "EFFN  11.415833",
+        "CKSUM 3564431818", "GA    8.00 7.20", "TC    8.00 7.20",
+        "NC    7.90 7.90", "STATS LOCAL MSV       -9.4043  0.71847",
+        "STATS LOCAL VITERBI   -9.7737  0.71847",
+        "STATS LOCAL FORWARD   -3.8341  0.71847" };
+  
+    for (String value : expected)
+    {
+      assertEquals(testScanner.nextLine(), value);
+    }
+  
+    testScanner.close();
+  }
+  
+  @Test(groups = "Functional")
+  public void testAppendModelAsString() throws FileNotFoundException
+  {
+    StringBuilder sb = new StringBuilder();
+    fn3.appendModelAsString(sb);
+    String string = sb.toString();
+
+    assertEquals(findValue(2, 2, 2, string), "4.42225");
+    assertEquals(findValue(12, 14, 1, string), "2.79307");
+    assertEquals(findValue(6, 24, 3, string), "0.48576");
+    assertEquals(findValue(19, 33, 2, string), "4.58477");
+    assertEquals(findValue(20, 64, 2, string), "3.61505");
+    assertEquals(findValue(3, 72, 3, string), "6.81068");
+    assertEquals(findValue(10, 80, 2, string), "2.69355");
+    assertEquals(findValue(16, 65, 1, string), "2.81003");
+    assertEquals(findValue(14, 3, 1, string), "2.69012");
+    assertEquals(findValue(11, 32, 1, string), "4.34805");
+  }
+  
+  /**
+   * A helper method to find a token in the model string
+   * 
+   * @param symbolIndex
+   *          index of symbol being searched. First symbol has index 1.
+   * @param nodeIndex
+   *          index of node being searched. Begin node has index 0. First node
+   *          has index 1.
+   * @param line
+   *          index of line being searched in node. First line has index 1.
+   * @param model
+   *          string model being searched
+   * @return value at specified position
+   */
+  private String findValue(int symbolIndex, int nodeIndex, int line,
+          String model)
+  {
+    String value = "";
+    Scanner scanner = new Scanner(model);
+    scanner.nextLine();
+    scanner.nextLine();
+  
+    for (int lineIndex = 0; lineIndex < line - 1; lineIndex++)
+    {
+      scanner.nextLine();
+    }
+    for (int node = 0; node < nodeIndex; node++)
+    {
+      scanner.nextLine();
+      scanner.nextLine();
+      scanner.nextLine();
+    }
+  
+    for (int symbol = 0; symbol < symbolIndex; symbol++)
+    {
+      value = scanner.next();
+      if ("COMPO".equals(value))
+      {
+        scanner.next();
+      }
+      else if (value.length() < 7)
+      {
+        scanner.next();
+      }
+    }
+    scanner.close();
+    return value;
+  }
+}
+
diff --git a/test/jalview/io/JSONFileTest.java b/test/jalview/io/JSONFileTest.java
index 158c901..4cd5b54 100644
--- a/test/jalview/io/JSONFileTest.java
+++ b/test/jalview/io/JSONFileTest.java
@@ -42,6 +42,7 @@ import jalview.schemes.ResidueColourScheme;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.HashMap;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 
@@ -205,7 +206,7 @@ public class JSONFileTest
     TEST_SEQ_HEIGHT = expectedSeqs.size();
     TEST_GRP_HEIGHT = expectedGrps.size();
     TEST_ANOT_HEIGHT = expectedAnnots.size();
-    TEST_CS_HEIGHT = expectedColSel.getHiddenColumnsCopy().size();
+    TEST_CS_HEIGHT = expectedColSel.getNumberOfRegions();
 
     exportSettings = new AlignExportSettingI()
     {
@@ -325,11 +326,12 @@ public class JSONFileTest
   {
     HiddenColumns cs = testJsonFile.getHiddenColumns();
     Assert.assertNotNull(cs);
-    Assert.assertNotNull(cs.getHiddenColumnsCopy());
-    List<int[]> hiddenCols = cs.getHiddenColumnsCopy();
-    Assert.assertEquals(hiddenCols.size(), TEST_CS_HEIGHT);
-    Assert.assertEquals(hiddenCols.get(0), expectedColSel
-            .getHiddenColumnsCopy().get(0),
+
+    Iterator<int[]> it = cs.iterator();
+    Iterator<int[]> colselit = expectedColSel.iterator();
+    Assert.assertTrue(it.hasNext());
+    Assert.assertEquals(cs.getNumberOfRegions(), TEST_CS_HEIGHT);
+    Assert.assertEquals(it.next(), colselit.next(),
             "Mismatched hidden columns!");
   }
 
@@ -492,8 +494,8 @@ public class JSONFileTest
             + actualGrp.getColourText());
     System.out.println(expectedGrp.getDisplayBoxes() + " | "
             + actualGrp.getDisplayBoxes());
-    System.out.println(expectedGrp.getIgnoreGapsConsensus() + " | "
-            + actualGrp.getIgnoreGapsConsensus());
+    System.out.println(expectedGrp.isIgnoreGapsConsensus() + " | "
+            + actualGrp.isIgnoreGapsConsensus());
     System.out.println(expectedGrp.getSequences().size() + " | "
             + actualGrp.getSequences().size());
     System.out.println(expectedGrp.getStartRes() + " | "
@@ -510,8 +512,8 @@ public class JSONFileTest
     if (expectedGrp.getName().equals(actualGrp.getName())
             && expectedGrp.getColourText() == actualGrp.getColourText()
             && expectedGrp.getDisplayBoxes() == actualGrp.getDisplayBoxes()
-            && expectedGrp.getIgnoreGapsConsensus() == actualGrp
-                    .getIgnoreGapsConsensus()
+            && expectedGrp.isIgnoreGapsConsensus() == actualGrp
+                    .isIgnoreGapsConsensus()
             && colourSchemeMatches
             && expectedGrp.getSequences().size() == actualGrp
                     .getSequences().size()
diff --git a/test/jalview/io/Jalview2xmlBase.java b/test/jalview/io/Jalview2xmlBase.java
index 15e18e3..fbdd782 100644
--- a/test/jalview/io/Jalview2xmlBase.java
+++ b/test/jalview/io/Jalview2xmlBase.java
@@ -76,7 +76,8 @@ public class Jalview2xmlBase
   @BeforeTest(alwaysRun = true)
   public static void clearDesktop()
   {
-    if (Desktop.instance != null && Desktop.getAlignFrames() != null)
+    if (Desktop.instance != null && Desktop.getFrames() != null
+            && Desktop.getFrames().length > 0)
     {
       Desktop.instance.closeAll_actionPerformed(null);
     }
diff --git a/test/jalview/io/Jalview2xmlTests.java b/test/jalview/io/Jalview2xmlTests.java
index e9e0782..41a6b89 100644
--- a/test/jalview/io/Jalview2xmlTests.java
+++ b/test/jalview/io/Jalview2xmlTests.java
@@ -44,7 +44,6 @@ import jalview.datamodel.features.FeatureMatcher;
 import jalview.datamodel.features.FeatureMatcherSet;
 import jalview.datamodel.features.FeatureMatcherSetI;
 import jalview.gui.AlignFrame;
-import jalview.gui.AlignViewport;
 import jalview.gui.AlignmentPanel;
 import jalview.gui.Desktop;
 import jalview.gui.FeatureRenderer;
@@ -771,7 +770,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/uniref50.fa", DataSourceType.FILE);
 
-    AlignViewport av = af.getViewport();
+    AlignViewportI av = af.getViewport();
     AlignmentI al = av.getAlignment();
 
     /*
diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java
index 4273e6c..1c9c79d 100644
--- a/test/jalview/io/StockholmFileTest.java
+++ b/test/jalview/io/StockholmFileTest.java
@@ -22,17 +22,22 @@ package jalview.io;
 
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertTrue;
 import static org.testng.AssertJUnit.fail;
 
+import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.gui.JvOptionPane;
 
 import java.io.File;
+import java.io.IOException;
 import java.util.Arrays;
 import java.util.BitSet;
 import java.util.HashMap;
@@ -230,8 +235,8 @@ public class StockholmFileTest
     // we might want to revise this in future
     int aa_new_size = (aa_new == null ? 0 : aa_new.length);
     int aa_original_size = (aa_original == null ? 0 : aa_original.length);
-    Map<Integer, BitSet> orig_groups = new HashMap<Integer, BitSet>();
-    Map<Integer, BitSet> new_groups = new HashMap<Integer, BitSet>();
+    Map<Integer, BitSet> orig_groups = new HashMap<>();
+    Map<Integer, BitSet> new_groups = new HashMap<>();
 
     if (aa_new != null && aa_original != null)
     {
@@ -654,4 +659,273 @@ public class StockholmFileTest
     testAlignmentEquivalence(al, newAl, true, true, true);
 
   }
+
+  @Test(groups = { "Functional" })
+  public void testTypeToDescription()
+  {
+    assertEquals("Secondary Structure",
+            StockholmFile.typeToDescription("SS"));
+    assertEquals("Surface Accessibility",
+            StockholmFile.typeToDescription("SA"));
+    assertEquals("transmembrane", StockholmFile.typeToDescription("TM"));
+    assertEquals("Posterior Probability",
+            StockholmFile.typeToDescription("PP"));
+    assertEquals("ligand binding", StockholmFile.typeToDescription("LI"));
+    assertEquals("active site", StockholmFile.typeToDescription("AS"));
+    assertEquals("intron", StockholmFile.typeToDescription("IN"));
+    assertEquals("interacting residue",
+            StockholmFile.typeToDescription("IR"));
+    assertEquals("accession", StockholmFile.typeToDescription("AC"));
+    assertEquals("organism", StockholmFile.typeToDescription("OS"));
+    assertEquals("class", StockholmFile.typeToDescription("CL"));
+    assertEquals("description", StockholmFile.typeToDescription("DE"));
+    assertEquals("reference", StockholmFile.typeToDescription("DR"));
+    assertEquals("look", StockholmFile.typeToDescription("LO"));
+    assertEquals("Reference Positions",
+            StockholmFile.typeToDescription("RF"));
+
+    // case-sensitive:
+    assertEquals("Rf", StockholmFile.typeToDescription("Rf"));
+    assertEquals("junk", StockholmFile.typeToDescription("junk"));
+    assertEquals("", StockholmFile.typeToDescription(""));
+    assertNull(StockholmFile.typeToDescription(null));
+  }
+
+  @Test(groups = { "Functional" })
+  public void testDescriptionToType()
+  {
+    assertEquals("SS",
+            StockholmFile.descriptionToType("Secondary Structure"));
+    assertEquals("SA",
+            StockholmFile.descriptionToType("Surface Accessibility"));
+    assertEquals("TM", StockholmFile.descriptionToType("transmembrane"));
+
+    // test is not case-sensitive:
+    assertEquals("SS",
+            StockholmFile.descriptionToType("secondary structure"));
+
+    // test is white-space sensitive:
+    assertNull(StockholmFile.descriptionToType("secondary structure "));
+
+    assertNull(StockholmFile.descriptionToType("any old junk"));
+    assertNull(StockholmFile.descriptionToType(""));
+    assertNull(StockholmFile.descriptionToType(null));
+  }
+
+  @Test(groups = { "Functional" })
+  public void testPrint()
+  {
+    SequenceI seq1 = new Sequence("seq1", "LKMF-RS-Q");
+    SequenceI seq2 = new Sequence("seq2/10-15", "RRS-LIP-");
+    SequenceI[] seqs = new SequenceI[] { seq1, seq2 };
+    AlignmentI al = new Alignment(seqs);
+
+    StockholmFile testee = new StockholmFile(al);
+
+    /*
+     * basic output (sequences only): 
+     * sequence ids are padded with 9 spaces more than the widest id
+     */
+    String output = testee.print(seqs, true);
+    String expected = "# STOCKHOLM 1.0\n" + "seq1/1-7           LKMF-RS-Q\n"
+            + "seq2/10-15         RRS-LIP-\n//\n";
+    assertEquals(expected, output);
+    
+    /*
+     * add some dbrefs
+     */
+    seq1.addDBRef(new DBRefEntry("PFAM", "1", "PF00111"));
+    seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "P83527"));
+    seq2.addDBRef(new DBRefEntry("RFAM", "1", "AY119185.1"));
+    seq2.addDBRef(new DBRefEntry("EMBL", "1", "AF125575"));
+    output = testee.print(seqs, true);
+    // PFAM and RFAM dbrefs should be output as AC, others as DR
+    expected = "# STOCKHOLM 1.0\n" + "#=GS seq1/1-7     AC PF00111\n"
+            + "#=GS seq1/1-7     DR UNIPROT ; P83527\n"
+            + "#=GS seq2/10-15   AC AY119185.1\n"
+            + "#=GS seq2/10-15   DR EMBL ; AF125575\n"
+            + "seq1/1-7           LKMF-RS-Q\n"
+            + "seq2/10-15         RRS-LIP-\n//\n";
+    assertEquals(expected, output);
+
+    /*
+     * add some sequence and alignment annotation
+     */
+    Annotation[] anns = new Annotation[5];
+    for (int i = 0; i < anns.length; i++)
+    {
+      anns[i] = new Annotation(String.valueOf((char) ('B' + i)),
+              "Desc " + i,
+              (char) ('C' + i), i + 3);
+    }
+
+    // expect "secondary structure" to be output as #=GR seqid SS
+    // using the secondary structure character (CDEFG) not display char (BCDEF)
+    AlignmentAnnotation aa1 = new AlignmentAnnotation("secondary structure",
+            "ssdesc", anns);
+    aa1.sequenceRef = seq1;
+    seq1.addAlignmentAnnotation(aa1);
+    al.addAnnotation(aa1);
+
+    // "sec structure" should not be output as no corresponding feature id
+    AlignmentAnnotation aa2 = new AlignmentAnnotation("sec structure",
+            "ssdesc", anns);
+    aa2.sequenceRef = seq2;
+    seq2.addAlignmentAnnotation(aa2);
+    al.addAnnotation(aa2);
+
+    // alignment annotation for Reference Positions: output as #=GC RF
+    AlignmentAnnotation aa3 = new AlignmentAnnotation("reference positions",
+            "refpos", anns);
+    al.addAnnotation(aa3);
+
+    // 'seq' annotation: output as seq_cons
+    AlignmentAnnotation aa4 = new AlignmentAnnotation("seq", "seqdesc",
+            anns);
+    al.addAnnotation(aa4);
+
+    // 'intron' annotation: output as IN_cons
+    AlignmentAnnotation aa5 = new AlignmentAnnotation("intron",
+            "introndesc", anns);
+    al.addAnnotation(aa5);
+
+    // 'binding site' annotation: output as binding_site
+    AlignmentAnnotation aa6 = new AlignmentAnnotation("binding site",
+            "bindingdesc", anns);
+    al.addAnnotation(aa6);
+
+    // 'autocalc' annotation should not be output
+    AlignmentAnnotation aa7 = new AlignmentAnnotation("Consensus",
+            "consensusdesc", anns);
+    aa7.autoCalculated = true;
+    al.addAnnotation(aa7);
+
+    // hidden annotation should not be output
+    AlignmentAnnotation aa8 = new AlignmentAnnotation("domains",
+            "domaindesc", anns);
+    aa8.visible = false;
+    al.addAnnotation(aa8);
+
+    output = testee.print(seqs, true);
+    //@formatter:off
+    expected = 
+            "# STOCKHOLM 1.0\n" 
+            + "#=GS seq1/1-7     AC PF00111\n"
+            + "#=GS seq1/1-7     DR UNIPROT ; P83527\n"
+            + "#=GS seq2/10-15   AC AY119185.1\n"
+            + "#=GS seq2/10-15   DR EMBL ; AF125575\n"
+            + "#=GR seq1/1-7 SS   CDEFG\n"
+            + "seq1/1-7           LKMF-RS-Q\n"
+            + "seq2/10-15         RRS-LIP-\n" 
+            + "#=GC RF            BCDEF\n" + "#=GC seq_cons      BCDEF\n"
+            + "#=GC IN_cons       BCDEF\n" + "#=GC binding_site  BCDEF\n"
+            + "//\n";
+    //@formatter:on
+    assertEquals(expected, output);
+  }
+
+  @Test(groups = "Functional")
+  public void testGetAnnotationCharacter()
+  {
+    SequenceI seq = new Sequence("seq", "abc--def-");
+
+    Annotation[] ann = new Annotation[8];
+    ann[1] = new Annotation("Z", "desc", 'E', 1f);
+    ann[2] = new Annotation("Q", "desc", ' ', 1f);
+    ann[4] = new Annotation("", "desc", 'E', 1f);
+    ann[6] = new Annotation("ZH", "desc", 'E', 1f);
+
+    /*
+     * null annotation in column (not Secondary Structure annotation)
+     * should answer sequence character, or '-' if null sequence
+     */
+    assertEquals('-',
+            StockholmFile.getAnnotationCharacter("RF", 0, ann[0], null));
+    assertEquals('d',
+            StockholmFile.getAnnotationCharacter("RF", 5, ann[5], seq));
+    assertEquals('-',
+            StockholmFile.getAnnotationCharacter("RF", 8, null, seq));
+
+    /*
+     * null annotation in column (SS annotation) should answer underscore
+     */
+    assertEquals('_',
+            StockholmFile.getAnnotationCharacter("SS", 0, ann[0], seq));
+
+    /*
+     * SS secondary structure symbol
+     */
+    assertEquals('E',
+            StockholmFile.getAnnotationCharacter("SS", 1, ann[1], seq));
+
+    /*
+     * no SS symbol, use label instead 
+     */
+    assertEquals('Q',
+            StockholmFile.getAnnotationCharacter("SS", 2, ann[2], seq));
+
+    /*
+     * SS with 2 character label - second character overrides SS symbol 
+     */
+    assertEquals('H',
+            StockholmFile.getAnnotationCharacter("SS", 6, ann[6], seq));
+
+    /*
+     * empty display character, not SS - answers '.'
+     */
+    assertEquals('.',
+            StockholmFile.getAnnotationCharacter("RF", 4, ann[4], seq));
+  }
+
+  /**
+   * Test to verify that gaps are input/output as underscore in STO annotation
+   * 
+   * @throws IOException
+   */
+  @Test(groups = "Functional")
+  public void testRoundtripWithGaps() throws IOException
+  {
+    /*
+     * small extract from RF00031_folded.stk
+     */
+    // @formatter:off
+    String stoData = 
+            "# STOCKHOLM 1.0\n" +
+            "#=GR B.taurus.4 SS .._((.))_\n" +
+            "B.taurus.4         AC.UGCGU.\n" +
+            "#=GR B.taurus.5 SS ..((_._))\n" +
+            "B.taurus.5         ACUU.G.CG\n" +
+        "//\n";
+    // @formatter:on
+    StockholmFile parser = new StockholmFile(stoData, DataSourceType.PASTE);
+    SequenceI[] seqs = parser.getSeqsAsArray();
+    assertEquals(2, seqs.length);
+
+    /*
+     * B.taurus.4 has a trailing gap
+     * rendered as underscore in Stockholm annotation
+     */
+    assertEquals("AC.UGCGU.", seqs[0].getSequenceAsString());
+    AlignmentAnnotation[] anns = seqs[0].getAnnotation();
+    assertEquals(1, anns.length);
+    AlignmentAnnotation taurus4SS = anns[0];
+    assertEquals(9, taurus4SS.annotations.length);
+    assertEquals(" .", taurus4SS.annotations[0].displayCharacter);
+    assertNull(taurus4SS.annotations[2]); // gapped position
+    assertNull(taurus4SS.annotations[8]); // gapped position
+    assertEquals('(', taurus4SS.annotations[3].secondaryStructure);
+    assertEquals("(", taurus4SS.annotations[3].displayCharacter);
+    assertEquals(')', taurus4SS.annotations[7].secondaryStructure);
+
+    /*
+     * output as Stockholm and verify it matches the original input
+     * (gaps output as underscore in annotation lines)
+     * note: roundtrip test works with the input lines ordered as above;
+     * can also parse in other orders, but then input doesn't match output
+     */
+    AlignmentFileWriterI afile = FileFormat.Stockholm
+            .getWriter(new Alignment(seqs));
+    String output = afile.print(seqs, false);
+    assertEquals(stoData, output);
+  }
 }
diff --git a/test/jalview/io/test_MADE1_hmm.txt b/test/jalview/io/test_MADE1_hmm.txt
new file mode 100644
index 0000000..32231db
--- /dev/null
+++ b/test/jalview/io/test_MADE1_hmm.txt
@@ -0,0 +1,268 @@
+HMMER3/f [3.1 | February 2013]
+NAME  MADE1
+ACC   DF0000629.2
+DESC  MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon
+LENG  80
+MAXL  426
+ALPH  DNA
+RF    yes
+MM    no
+CONS  yes
+CS    no
+MAP   yes
+DATE  Tue Feb 19 20:33:41 2013
+NSEQ  1997
+EFFN  3.911818
+CKSUM 3015610723
+GA 2.324 4.234
+TC 2.343 1.212
+NC 2.354 5.456
+STATS LOCAL MSV       -8.5786  0.71858
+STATS LOCAL VITERBI   -9.3632  0.71858
+STATS LOCAL FORWARD   -3.4823  0.71858
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.24257  1.59430  1.62906  1.16413
+          1.38629  1.38629  1.38629  1.38629
+          0.03960  3.94183  3.94183  1.46634  0.26236  0.00000        *
+      1   2.69765  2.44396  2.81521  0.24089      1 t x - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03960  3.94183  3.94183  1.46634  0.26236  1.09861  0.40547
+      2   2.72939  2.37873  2.85832  0.24244      2 t x - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03725  4.00179  4.00179  1.46634  0.26236  1.09861  0.40547
+      3   0.16099  3.16370  2.87328  2.99734      3 a x - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03604  4.03416  4.03416  1.46634  0.26236  1.09861  0.40547
+      4   1.98862  2.42132  0.42649  2.10770      4 g x - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03539  4.05203  4.05203  1.46634  0.26236  1.09861  0.40547
+      5   1.96369  2.69532  0.36534  2.32099      5 g x - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03764  4.06427  3.92372  1.46634  0.26236  1.09861  0.40547
+      6   2.56994  2.11239  2.71946  0.30571      6 t x - -
+          1.37159  1.41129  1.39124  1.37159
+          0.03806  3.89715  4.07214  1.50442  0.25122  1.00714  0.45454
+      7   2.58388  2.10353  2.64646  0.31253     12 t x - -
+          1.38764  1.38524  1.38764  1.38465
+          0.03494  4.03864  4.09125  1.40070  0.28293  1.09237  0.40860
+      8   2.18552  2.70201  0.28821  2.64645     14 g x - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03628  4.09157  3.96779  1.46634  0.26236  1.09861  0.40547
+      9   2.16916  2.82142  0.28427  2.60854     15 g x - -
+          1.38091  1.39033  1.38365  1.39033
+          0.03566  4.00237  4.08886  1.38021  0.28972  1.01958  0.44745
+     10   2.45517  2.15232  2.42886  0.34277     18 t x - -
+          1.39065  1.39065  1.39065  1.37335
+          0.03536  4.01212  4.09576  1.39554  0.28462  1.09775  0.40589
+     11   2.10260  2.95484  0.28160  2.64222     21 g x - -
+          1.36740  1.40555  1.40555  1.36740
+          0.03843  3.92069  4.02468  1.44733  0.26814  1.09856  0.40549
+     12   2.54740  0.30185  2.61355  2.21647     26 c x - -
+          1.38748  1.38276  1.38748  1.38748
+          0.03457  4.05446  4.09623  1.40847  0.28040  1.05496  0.42803
+     13   0.28443  2.72003  2.32214  2.48149     28 a x - -
+          1.38740  1.38740  1.38298  1.38740
+          0.03441  4.05976  4.10001  1.41198  0.27926  1.09780  0.40587
+     14   0.29412  2.55413  2.49679  2.35701     30 a x - -
+          1.38194  1.39067  1.38194  1.39067
+          0.03505  4.02482  4.10005  1.39522  0.28473  1.09929  0.40512
+     15   0.18837  2.99710  2.82270  2.77556     33 a x - -
+          1.39015  1.39472  1.37503  1.38539
+          0.03725  3.97815  4.02618  1.37955  0.28994  1.10102  0.40426
+     16   0.50816  2.05151  2.22111  1.82407     37 a x - -
+          1.36727  1.38730  1.39683  1.39405
+          0.04830  3.89881  3.61610  1.29026  0.32186  1.05306  0.42905
+     17   2.11260  2.73141  0.29747  2.64152     41 g x - -
+          1.36913  1.40376  1.40376  1.36913
+          0.03705  3.93681  4.08299  1.44872  0.26771  1.07479  0.41759
+     18   2.24459  1.90539  2.34054  0.43234     46 t x - -
+          1.33632  1.42493  1.39937  1.38665
+          0.04427  3.64574  4.06297  1.70501  0.20061  1.21309  0.35279
+     19   0.44322  2.17202  2.18055  2.03175     57 a x - -
+          1.41047  1.41471  1.36338  1.35797
+          0.03970  3.81957  4.07540  1.65588  0.21186  1.22788  0.34660
+     20   0.33340  2.42691  2.40824  2.25160     66 a x - -
+          1.29389  1.44615  1.37917  1.43324
+          0.04223  3.70146  4.09459  1.55158  0.23815  1.05880  0.42598
+     21   2.50563  1.98543  2.69601  0.33746     74 t x - -
+          1.39462  1.39462  1.42862  1.32990
+          0.04184  3.80216  3.98177  1.80466  0.17976  1.00279  0.45705
+     22   2.54484  1.97505  2.66483  0.33806     84 t x - -
+          1.39134  1.39489  1.38662  1.37246
+          0.03877  3.97504  3.95038  1.37620  0.29107  1.13932  0.38572
+     23   2.10159  2.83856  0.29282  2.61635     88 g x - -
+          1.39682  1.39682  1.35536  1.39682
+          0.05046  3.75402  3.65808  1.08330  0.41321  1.13019  0.39004
+     24   2.25298  0.61854  2.50691  1.29221     90 c x - -
+          1.35803  1.49605  1.46737  1.24379
+          0.06091  3.28322  3.83564  1.89752  0.16245  1.28788  0.32276
+     25   1.27819  2.23285  0.76242  1.91259    106 g x - -
+          1.29024  1.67349  1.68279  1.04597
+          0.05752  3.44263  3.73311  2.58671  0.07825  1.26818  0.33037
+     26   1.86925  2.58352  0.39466  2.33986    131 g x - -
+          1.31084  1.49412  1.46666  1.29002
+          0.04698  3.54257  4.07715  2.25245  0.11109  0.86163  0.54900
+     27   2.38297  1.93394  2.39162  0.39800    151 t x - -
+          1.33582  1.47359  1.44163  1.30411
+          0.04951  3.48445  4.03783  2.15951  0.12260  1.21681  0.35122
+     28   2.41717  2.17810  2.62774  0.32113    170 t x - -
+          1.36805  1.48060  1.37439  1.32840
+          0.04849  3.50958  4.05014  2.58370  0.07850  1.22399  0.34822
+     29   2.57764  2.35132  2.56552  0.28512    194 t x - -
+          1.43829  1.43458  1.24787  1.43829
+          0.04667  3.56670  4.05428  2.49706  0.08591  1.23744  0.34267
+     30   2.47248  2.07688  2.62257  0.33172    215 t x - -
+          1.25120  1.52623  1.70635  1.15531
+          0.08932  3.31524  3.01336  2.81842  0.06156  1.22909  0.34610
+     31   2.25937  2.13157  2.02027  0.43957    248 t x - -
+          1.18172  1.43522  1.72841  1.28150
+          0.07936  2.93117  3.77395  2.46269  0.08906  0.60457  0.79034
+     32   2.04508  2.84981  0.30490  2.58263    280 g x - -
+          1.17665  1.66785  1.66218  1.16056
+          0.05998  3.23615  3.96853  2.83684  0.06040  1.01952  0.44749
+     33   2.45103  0.38098  2.56776  1.87147    317 c x - -
+          1.24153  1.52524  1.60663  1.22783
+          0.05538  3.39046  3.90294  2.73920  0.06680  1.18729  0.36391
+     34   2.22082  0.36258  2.75077  2.02704    347 c x - -
+          1.15008  1.62014  1.86511  1.10673
+          0.06086  3.18178  4.04341  2.94504  0.05403  1.25991  0.33363
+     35   0.27033  2.66664  2.52541  2.43767    388 a x - -
+          1.24951  1.47565  1.41392  1.42074
+          0.07123  3.00373  3.95552  3.13655  0.04440  1.28173  0.32512
+     36   2.83107  2.41670  2.97197  0.22235    439 t x - -
+          1.37071  1.57683  1.38637  1.23972
+          0.05293  3.45216  3.91807  2.54402  0.08181  1.14651  0.38235
+     37   2.52322  2.25084  2.45909  0.31611    465 t x - -
+          1.26335  1.55077  1.59008  1.19965
+          0.07504  3.13329  3.55006  3.08962  0.04659  1.13108  0.38962
+     38   0.45807  2.30687  1.98940  2.03143    512 a x - -
+          1.15472  1.67511  1.53797  1.26320
+          0.09820  3.13076  2.99876  2.79197  0.06326  1.39915  0.28343
+     39   2.37471  0.42180  2.44763  1.80427    550 c x - -
+          1.23785  1.49058  1.48364  1.35502
+          0.06081  3.19472  4.01643  2.41851  0.09327  0.94671  0.49105
+     40   2.32826  1.95481  2.36781  0.40458    578 t x - -
+          1.36586  1.46001  1.43000  1.29720
+          0.05257  3.39673  4.03256  1.84862  0.17133  1.40979  0.27997
+     41   2.68669  2.13935  2.81520  0.28200    592 t x - -
+          1.34965  1.42793  1.45781  1.31633
+          0.04735  3.57826  3.99988  2.09424  0.13144  1.22129  0.34934
+     42   2.55904  2.16444  2.70859  0.29952    609 t x - -
+          1.12072  1.61936  1.63578  1.26895
+          0.07346  3.25910  3.42962  2.85641  0.05919  1.38363  0.28857
+     43   1.99923  1.61027  2.26343  0.57851    646 t x - -
+          1.32290  1.58747  1.61095  1.11018
+          0.06656  3.08568  3.97944  2.44774  0.09046  0.75593  0.63407
+     44   0.23887  2.79899  2.55209  2.60783    675 a x - -
+          1.18557  1.50323  1.59070  1.31590
+          0.05597  3.38637  3.88222  2.46900  0.08847  1.27945  0.32599
+     45   0.29593  2.53488  2.53903  2.32335    701 a x - -
+          1.08710  1.54222  1.59276  1.40430
+          0.07539  2.94521  3.91062  1.91623  0.15918  1.22327  0.34852
+     46   2.58352  2.40524  2.76700  0.25955    725 t x - -
+          1.19685  1.58503  1.74852  1.14293
+          0.06124  3.18279  4.02089  2.82961  0.06085  1.05474  0.42814
+     47   2.13251  2.88788  0.29508  2.50964    764 g x - -
+          1.20891  1.55463  1.68206  1.19000
+          0.06526  3.12574  3.94910  2.41448  0.09367  1.10396  0.40280
+     48   2.23841  2.99164  0.25118  2.72900    792 g x - -
+          1.26330  1.55339  1.52606  1.24355
+          0.05464  3.34968  4.01313  2.78872  0.06347  1.15133  0.38012
+     49   2.57533  0.32900  2.64632  2.01501    824 c x - -
+          1.35118  1.39828  1.40141  1.39516
+          0.04340  3.79297  3.91506  1.59549  0.22666  1.20075  0.35806
+     50   0.46433  2.04127  2.23437  2.00605    833 a x - -
+          1.23062  1.36903  1.62282  1.36182
+          0.05764  3.31530  3.92762  2.28791  0.10700  1.07910  0.41536
+     51   0.27513  2.77017  2.28518  2.57549    853 a x - -
+          1.27958  1.58726  1.46109  1.25394
+          0.05750  3.30072  3.96214  2.60776  0.07656  1.25708  0.33475
+     52   0.20149  2.86434  2.84551  2.69770    883 a x - -
+          1.23645  1.62259  1.71174  1.10368
+          0.05756  3.26729  4.02702  2.54508  0.08172  1.27391  0.32814
+     53   0.26982  2.65833  2.50477  2.46835    911 a x - -
+          1.36005  1.50358  1.48100  1.22550
+          0.06921  3.37553  3.42118  2.36646  0.09851  1.27560  0.32748
+     54   0.40022  2.19284  2.22687  2.20396    934 a x - -
+          1.12070  1.60472  1.53213  1.35895
+          0.05523  3.36752  3.94966  2.42917  0.09224  0.84774  0.55928
+     55   2.11356  0.46400  2.46442  1.79955    960 c x - -
+          1.23932  1.35913  1.50478  1.46331
+          0.05187  3.47055  3.94022  2.35854  0.09933  1.12102  0.39445
+     56   1.85868  0.79440  2.22069  1.25971    983 c x - -
+          1.21951  1.50212  1.51138  1.34185
+          0.06404  3.29054  3.69705  1.75742  0.18933  1.18410  0.36532
+     57   1.33272  2.32720  0.71452  1.90215    999 g x - -
+          1.12229  1.49343  1.56653  1.42255
+          0.04920  3.46654  4.08749  2.17995  0.11996  1.31769  0.31164
+     58   2.48337  0.43652  2.46331  1.68683   1017 c x - -
+          1.34704  1.55461  1.38112  1.28222
+          0.04823  3.61532  3.90311  2.20911  0.11631  1.00864  0.45368
+     59   0.41659  2.44509  1.93972  2.20507   1034 a x - -
+          1.38198  1.38198  1.39194  1.38932
+          0.03641  3.98130  4.06929  1.35873  0.29704  1.31330  0.31325
+     60   0.41612  2.39160  1.97116  2.21075   1037 a x - -
+          1.03649  1.46430  1.57421  1.57557
+          0.04769  3.52580  4.06641  2.32461  0.10294  0.84329  0.56263
+     61   2.66264  2.12302  2.82746  0.28581   1056 t x - -
+          1.36925  1.39635  1.38930  1.39048
+          0.04097  3.97400  3.84718  1.39433  0.28502  1.12205  0.39395
+     62   2.26510  2.13196  2.42551  0.37231   1060 t x - -
+          1.37965  1.39147  1.39147  1.38264
+          0.04082  3.91610  3.90805  1.24613  0.33914  0.95192  0.48776
+     63   0.41244  2.25761  2.16787  2.12907   1062 a x - -
+          1.34515  1.41203  1.41203  1.37753
+          0.04054  3.77835  4.08203  1.30483  0.31638  1.11819  0.39582
+     64   2.51464  0.37905  2.62296  1.82008   1068 c x - -
+          1.39543  1.38753  1.39233  1.37008
+          0.03854  3.90584  4.03535  1.36573  0.29463  1.13682  0.38689
+     65   2.16380  2.11332  2.18714  0.42765   1073 t x - -
+          1.38764  1.38471  1.38519  1.38764
+          0.03575  4.05376  4.03073  1.40080  0.28289  1.03825  0.43707
+     66   2.79349  2.39141  2.87271  0.23478   1075 t x - -
+          1.37227  1.39101  1.39101  1.39101
+          0.03597  4.01447  4.05827  1.39017  0.28639  1.06429  0.42308
+     67   2.82488  2.47749  2.93179  0.21887   1078 t x - -
+          1.38141  1.39112  1.38915  1.38353
+          0.03661  3.99477  4.04370  1.35958  0.29675  1.13439  0.38804
+     68   2.77679  2.30433  2.90694  0.24425   1081 t x - -
+          1.37593  1.38989  1.45520  1.32825
+          0.04447  3.68736  3.99242  1.76176  0.18843  0.98580  0.46703
+     69   2.47698  3.17398  0.19595  2.95437   1093 g x - -
+          1.38264  1.38264  1.39734  1.38264
+          0.05358  3.96553  3.40487  1.40348  0.28202  1.03112  0.44100
+     70   2.84327  0.27906  2.97336  2.00890   1097 c x - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03412  4.08811  4.08811  1.46634  0.26236  0.69006  0.69625
+     71   0.21870  2.83638  2.69251  2.65798   1098 a x - -
+          1.37446  1.37942  1.39640  1.39509
+          0.03670  3.93983  4.09935  1.41905  0.27700  1.10002  0.40476
+     72   2.35233  0.46085  2.23804  1.78715   1103 c x - -
+          1.38536  1.38781  1.38781  1.38421
+          0.03493  4.03822  4.09272  1.39310  0.28542  1.09638  0.40658
+     73   2.57111  0.32543  2.74124  1.98892   1105 c x - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03381  4.09688  4.09688  1.46634  0.26236  1.09626  0.40664
+     74   0.27014  2.61416  2.53262  2.47636   1106 a x - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03461  4.09267  4.05587  1.46634  0.26236  1.09748  0.40603
+     75   0.52873  2.16549  1.91736  1.90409   1107 a x - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03426  4.08396  4.08396  1.46634  0.26236  1.07423  0.41788
+     76   2.33134  0.38082  2.65861  1.90055   1108 c x - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03466  4.07266  4.07266  1.46634  0.26236  1.09861  0.40547
+     77   2.20588  0.45134  2.35553  1.84373   1109 c x - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03550  4.04912  4.04912  1.46634  0.26236  1.09861  0.40547
+     78   2.69018  2.22054  2.82311  0.26898   1110 t x - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03711  4.00561  4.00561  1.46634  0.26236  1.09861  0.40547
+     79   0.16248  3.15867  2.86159  2.98963   1111 a x - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04048  3.92018  3.92018  1.46634  0.26236  1.09861  0.40547
+     80   0.17484  3.04770  2.86638  2.88183   1112 a x - -
+          1.38629  1.38629  1.38629  1.38629
+          0.02045  3.90014        *  1.46634  0.26236  0.00000        *
+//
diff --git a/test/jalview/io/test_PKinase_hmm.txt b/test/jalview/io/test_PKinase_hmm.txt
new file mode 100644
index 0000000..e1ad9f9
--- /dev/null
+++ b/test/jalview/io/test_PKinase_hmm.txt
@@ -0,0 +1,806 @@
+HMMER3/e [3.0 | March 2010]
+NAME  Pkinase
+ACC   PF00069.17
+DESC  Protein kinase domain
+LENG  260
+ALPH  amino
+RF    no
+CONS  yes
+CS    yes
+MAP   yes
+DATE  Thu Jun 16 11:44:06 2011
+NSEQ  54
+EFFN  3.358521
+CKSUM 3106786190
+GA    70.30 70.30
+TC    70.30 70.30
+NC    70.20 70.20
+STATS LOCAL MSV      -10.7215  0.70254
+STATS LOCAL VITERBI  -11.6541  0.70254
+STATS LOCAL FORWARD   -5.2305  0.70254
+HMM          A        C        D        E        F        G        H        I        K        L        M        N        P        Q        R        S        T        V        W        Y   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   2.60017  4.19886  2.94089  2.63789  3.35087  2.89119  3.48337  2.79435  2.60265  2.43454  3.62613  3.06133  3.41286  3.09693  2.94507  2.65650  2.87761  2.67871  4.54052  3.43274
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00990  5.01631  5.73865  0.61958  0.77255  0.00000        *
+      1   2.91704  4.31028  4.76351  3.63148  2.10912  3.47710  4.39734  2.27639  3.96619  1.99282  3.42844  4.19567  4.43771  4.11903  3.67403  3.22736  3.14918  2.35905  3.32515  1.82622      1 y - - E
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00990  5.01631  5.73865  0.61958  0.77255  0.48576  0.95510
+      2   2.77204  4.20708  3.06476  1.97968  4.66603  3.66509  3.19858  3.37903  2.25347  3.34018  4.38833  2.97180  4.05804  2.36838  2.43173  2.67542  2.50268  2.83403  5.78758  4.38976      2 e - - E
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00990  5.01631  5.73865  0.61958  0.77255  0.48576  0.95510
+      3   2.90076  4.04294  3.31590  2.80413  3.08157  3.87481  4.12616  2.18958  2.49735  1.97194  3.73714  3.32717  3.98753  3.23115  3.12315  2.99137  2.62008  2.29426  5.21478  3.75979      3 l - - E
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00990  5.01631  5.73865  0.61958  0.77255  0.48576  0.95510
+      4   2.89383  4.85429  3.10311  2.63174  3.71383  2.56808  3.47232  2.82076  2.61844  1.98342  3.72320  3.05498  4.17347  3.05527  3.32194  2.85608  2.93671  2.18878  5.40057  3.87183      4 l - - E
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00990  5.01631  5.73865  0.61958  0.77255  0.48576  0.95510
+      5   2.68261  5.39185  2.80437  1.87471  4.73638  2.79887  3.69591  4.22191  2.19487  3.69685  4.08896  3.12413  3.70490  2.48424  2.08916  2.53260  3.02309  3.43812  5.82480  4.41426      5 e - - E
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00990  5.01631  5.73865  0.61958  0.77255  0.48576  0.95510
+      6   2.77253  4.06085  3.07881  2.53373  4.10647  3.71564  3.68370  2.64290  2.00036  2.72968  4.17370  3.24239  3.08607  2.77632  2.72820  2.69921  2.54335  2.71931  5.60386  4.26496      6 k - - E
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00990  5.01631  5.73865  0.61958  0.77255  0.48576  0.95510
+      7   3.42930  4.74416  5.34765  4.76823  3.71832  4.71430  5.09461  1.33015  3.54417  1.12594  3.33523  4.84641  5.00427  4.73010  4.64986  4.05097  3.66327  1.83083  5.51142  4.37013      7 l - - E
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+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00990  5.01631  5.73865  0.61958  0.77255  0.48576  0.95510
+    163   2.71301  5.29924  2.59488  2.14743  3.52695  3.04037  3.28275  4.06670  2.61594  3.34508  4.35002  2.84026  3.31113  2.97459  2.36266  2.86533  2.70674  3.41928  3.03699  3.23042    296 e - - G
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00990  5.01631  5.73865  0.61958  0.77255  0.48576  0.95510
+    164   4.65993  5.73598  5.69662  5.49898  1.97465  5.32012  3.31709  4.36240  5.29326  3.66395  4.92323  4.93743  5.59573  5.06816  5.17473  4.69695  3.41633  4.25844  2.61302  0.51590    297 Y - - G
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00990  5.01631  5.73865  0.61958  0.77255  0.48576  0.95510
+    165   2.46851  3.63596  4.34730  3.76113  3.49978  4.00900  4.30977  2.55613  3.41377  2.11254  1.89168  3.40620  4.37893  3.86942  2.23584  3.08926  3.14320  2.13937  5.00600  3.81292    298 m - - S
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00990  5.01631  5.73865  0.61958  0.77255  0.48576  0.95510
+    166   0.54633  4.79516  4.59072  4.34047  5.33605  3.22550  5.27451  4.80651  4.37656  4.47607  5.24769  4.21379  3.02084  4.58677  4.60871  1.81435  3.40538  4.05386  6.66459  5.53199    299 A - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00990  5.01631  5.73865  0.61958  0.77255  0.48576  0.95510
+    167   3.08666  5.02380  4.02349  3.92167  5.10908  3.73669  5.07487  4.62556  4.04836  4.33998  5.22795  3.34786  0.41351  4.38870  4.30726  3.26072  3.60085  3.40472  6.47905  5.20179    300 P - - H
+          2.68622  4.42144  2.77523  2.73111  3.46358  2.40517  3.72498  3.29358  2.67745  2.69359  4.24694  2.90351  2.73743  3.18126  2.89786  2.37891  2.77523  2.98522  4.58481  3.61507
+          0.03484  3.47295  5.73865  0.99675  0.46057  0.48576  0.95510
+    168   3.66837  6.19086  2.84947  0.45189  5.55161  3.90523  4.43200  5.09782  3.30487  4.55035  5.42336  3.03786  4.53514  3.60153  3.37398  3.54999  3.95969  4.65772  6.64024  5.17650    305 E - - H
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00990  5.01631  5.73865  0.61958  0.77255  0.48576  0.95510 
+    169   2.79774  4.32598  4.68241  3.67608  3.42171  4.06471  4.38713  2.01470  3.90321  1.87174  3.44282  4.15860  4.43014  3.77035  3.25202  3.36713  2.95239  1.31877  3.77234  3.76466    306 v - - H
+          2.68603  4.42242  2.77519  2.73104  3.46342  2.40506  3.72511  3.29371  2.67728  2.69322  4.24707  2.90364  2.73756  3.18163  2.89801  2.37893  2.77519  2.98535  4.58494  3.61520
+          0.12919  2.22240  4.35495  1.23224  0.34480  0.48576  0.95510
+    170   2.91184  3.76308  4.76588  4.15799  3.39752  4.06920  3.82796  1.60071  3.96642  1.39613  3.17824  3.65225  4.43387  4.11848  4.01348  2.94594  3.14403  2.21737  4.92444  3.43929    311 l - - H
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00999  5.00664  5.72898  0.61958  0.77255  0.51297  0.91308
+    171   2.62785  5.06480  3.29796  2.67561  3.73804  3.41086  3.92577  3.21358  2.32640  2.15096  3.31180  2.55443  4.11004  2.47045  2.33927  2.70318  3.11578  3.12852  5.57146  4.24107    312 l - - C
+          2.68631  4.42245  2.77511  2.73076  3.46350  2.40522  3.72547  3.29356  2.67765  2.69366  4.24573  2.90389  2.73738  3.18142  2.89826  2.37846  2.77520  2.98520  4.58530  3.61473
+          0.62427  1.87899  1.16602  1.98855  0.14722  0.46912  0.98231
+    172   2.60166  5.18307  2.62016  2.19793  3.35206  2.39740  3.57105  3.96340  2.18128  3.47543  4.23188  3.01161  3.92489  2.82990  2.86326  2.33987  2.67701  3.55746  5.63416  3.78538    327 k - - C
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.01428  4.65191  5.37425  0.61958  0.77255  0.24611  1.52250
+    173   2.37600  3.94341  2.81761  2.45806  4.08381  2.38833  3.32666  4.15213  2.47322  3.64753  4.39446  2.71786  3.74359  2.39493  2.76163  2.38666  3.00597  3.01776  5.79219  3.82026    328 a - - S
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00998  5.00778  5.73012  0.61958  0.77255  0.47101  0.97916
+    174   2.81816  4.87774  2.88922  2.34131  3.91699  3.47934  3.84840  3.76601  2.22767  3.10881  4.41163  2.46519  2.75598  2.51039  2.43545  2.43680  2.76354  3.54179  5.80719  3.84984    329 k - - -
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+          0.00990  5.01631  5.73865  0.61958  0.77255  0.48576  0.95510
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+          0.00990  5.01631  5.73865  0.61958  0.77255  0.48576  0.95510
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+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00990  5.01631  5.73865  0.61958  0.77255  0.48576  0.95510
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+          0.00990  5.01631  5.73865  0.61958  0.77255  0.48576  0.95510
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+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00990  5.01631  5.73865  0.61958  0.77255  0.48576  0.95510
+    179   2.27957  5.36842  3.14470  2.24142  4.70283  3.35867  3.70433  4.18054  1.84880  3.00297  4.41216  3.13478  2.50109  2.87247  2.49374  2.50485  2.88881  3.75338  5.80713  4.40386    334 k - - H
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+          0.00990  5.01631  5.73865  0.61958  0.77255  0.48576  0.95510
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+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00990  5.01631  5.73865  0.61958  0.77255  0.48576  0.95510
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+          0.00990  5.01631  5.73865  0.61958  0.77255  0.48576  0.95510
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+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00990  5.01631  5.73865  0.61958  0.77255  0.48576  0.95510
+    183   4.60767  5.71652  5.61554  3.89031  2.18526  5.28181  4.15190  4.32304  5.18037  3.62888  4.88484  4.90634  5.56392  5.01906  5.10312  4.65700  4.81381  4.22147  0.60655  1.74323    338 W - - H
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00990  5.01631  5.73865  0.61958  0.77255  0.48576  0.95510
+    184   1.30551  4.78823  4.65738  4.37945  5.36630  2.58206  5.28849  4.84019  4.38318  4.50739  5.27020  4.22569  4.39579  4.59600  4.61395  0.79404  2.89139  4.06528  6.68751  5.56026    339 s - - H
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+          0.00990  5.01631  5.73865  0.61958  0.77255  0.48576  0.95510
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+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00990  5.01631  5.73865  0.61958  0.77255  0.48576  0.95510
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+          0.00990  5.01631  5.73865  0.61958  0.77255  0.48576  0.95510
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+          0.00990  5.01631  5.73865  0.61958  0.77255  0.48576  0.95510
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+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00990  5.01631  5.73865  0.61958  0.77255  0.48576  0.95510
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+          0.00990  5.01631  5.73865  0.61958  0.77255  0.48576  0.95510
+    191   2.65126  3.79080  3.03118  1.37895  4.54227  3.68257  3.87660  3.27048  2.56225  3.53374  4.30787  2.88399  4.07460  2.72714  3.11894  2.49943  2.86114  3.20681  5.71940  3.61825    346 e - - H
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
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+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
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+          0.00990  5.01631  5.73865  0.61958  0.77255  0.48576  0.95510
+    255   2.91099  3.35807  4.39311  3.80506  3.12662  3.41984  4.32058  2.74098  2.62412  1.35983  2.89439  3.70896  4.38574  3.55146  3.43970  3.02120  3.14303  2.30767  4.99433  3.18557    471 l - - H
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00990  5.01631  5.73865  0.61958  0.77255  0.48576  0.95510
+    256   2.62697  4.23577  2.94369  2.01671  4.73311  3.52212  3.12192  4.21804  1.98366  3.41966  4.43054  2.33684  4.05005  2.29561  2.80226  2.65814  2.90658  3.41449  5.82302  4.41298    472 k - - T
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00990  5.01631  5.73865  0.61958  0.77255  0.48576  0.95510
+    257   2.67425  5.24257  2.69003  2.64384  4.09422  3.68496  1.59772  3.97575  2.52719  3.06621  3.97630  3.17995  4.07682  2.88982  2.86815  2.31165  2.78826  3.60139  5.71188  4.10399    473 h - - S
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.18941  5.01631  1.79622  0.61958  0.77255  0.48576  0.95510
+    258   2.81850  5.23743  2.76502  2.35780  4.54654  3.39495  3.79640  3.57339  2.36240  3.35446  4.28834  3.08690  1.61434  2.83455  2.79066  2.56844  3.04975  3.37601  5.69198  4.30446    474 p - - G
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.01183  4.83873  5.56107  0.61958  0.77255  0.86853  0.54398
+    259   3.22678  4.58175  4.94227  4.40609  1.73776  4.31983  4.20406  3.01156  4.21650  2.23279  3.33965  4.33985  4.66520  3.80636  4.24184  3.63704  3.45535  2.61441  1.69956  1.91736    475 w - - G
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.01183  4.83873  5.56107  0.61958  0.77255  0.30436  1.33787
+    260   2.99670  4.36610  4.95290  4.33956  1.72799  3.71830  4.50360  1.92619  4.12878  1.69258  2.79907  4.33234  4.52551  4.25179  4.13733  3.48573  3.22794  1.98896  4.25850  3.81122    476 l - - G
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00667  5.01308        *  0.61958  0.77255  0.00000        *
+//
diff --git a/test/jalview/io/test_fn3_hmm.txt b/test/jalview/io/test_fn3_hmm.txt
new file mode 100644
index 0000000..0dcfa22
--- /dev/null
+++ b/test/jalview/io/test_fn3_hmm.txt
@@ -0,0 +1,285 @@
+HMMER3/f [3.1b1 | May 2013]
+NAME  fn3
+ACC   PF00041.13
+DESC  Fibronectin type III domain
+LENG  86
+ALPH  amino
+RF    no
+MM    no
+CONS  yes
+CS    yes
+MAP   yes
+DATE  Fri Jun 20 08:22:31 2014
+NSEQ  106
+EFFN  11.415833
+CKSUM 3564431818
+GA    8.00 7.20
+TC    8.00 7.20
+NC    7.90 7.90
+STATS LOCAL MSV       -9.4043  0.71847
+STATS LOCAL VITERBI   -9.7737  0.71847
+STATS LOCAL FORWARD   -3.8341  0.71847
+HMM          A        C        D        E        F        G        H        I        K        L        M        N        P        Q        R        S        T        V        W        Y   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   2.70330  4.91262  3.03272  2.64079  3.60307  2.84344  3.74204  3.07942  2.79841  2.65364  4.14864  2.95826  2.87120  3.02176  2.96125  2.44783  2.59757  2.57680  4.02726  3.21526
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00338  6.08833  6.81068  0.61958  0.77255  0.00000        *
+      1   3.16986  5.21447  4.52134  3.29953  4.34285  4.18764  4.30886  3.35801  3.70246  2.11675  4.32057  4.32984  0.76706  3.91880  4.22437  3.23552  3.21670  2.88223  5.80355  3.93889      1 p - - -
+          2.68629  4.42236  2.77530  2.73088  3.46365  2.40512  3.72505  3.29365  2.67737  2.69316  4.24701  2.90358  2.73734  3.18157  2.89812  2.37898  2.77517  2.98515  4.58488  3.61514
+          0.09796  2.38361  6.81068  0.10064  2.34607  0.48576  0.95510
+      2   2.70230  5.97353  2.24744  2.62947  5.31433  2.60356  4.43584  4.79731  3.17221  2.95090  5.01531  3.26630  2.09873  3.30219  3.34190  1.45782  3.14099  3.57507  6.40877  4.25623      3 s - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00338  6.08833  6.81068  0.61958  0.77255  0.48576  0.95510
+      3   1.38116  5.98285  3.50784  2.54546  5.32790  3.48945  4.43311  4.81385  2.38773  3.98773  5.02352  3.27895  1.92260  2.69012  2.96119  2.64228  3.29228  3.29618  6.41555  4.20553      4 a - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00338  6.08833  6.81068  0.61958  0.77255  0.48576  0.95510
+      4   3.32856  5.10403  4.47046  4.60386  4.23079  4.75438  5.09647  2.69918  4.46632  2.97102  4.23502  4.77984  0.63388  4.68581  3.76781  4.05413  3.46306  2.04533  5.75329  4.56372      5 P - - -
+          2.68616  4.42236  2.77530  2.73134  3.46365  2.40523  3.72505  3.29295  2.67751  2.69303  4.24634  2.90357  2.73739  3.18157  2.89783  2.37897  2.77530  2.98529  4.58488  3.61514
+          0.09682  2.39494  6.81068  0.10162  2.33687  0.48576  0.95510
+      5   2.95325  4.65976  3.57762  2.20709  3.14816  2.51487  3.41109  4.78902  2.65862  3.19599  4.41042  3.45032  3.44719  2.43205  2.26492  2.25400  2.23196  3.66828  4.80003  4.52485      7 e - - C
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.01246  6.08833  4.59386  0.61958  0.77255  0.48576  0.95510
+      6   2.74215  5.97618  2.19482  2.69150  4.58171  2.33553  3.83525  3.28222  2.95080  3.32698  5.01691  1.45822  3.52462  2.79670  2.90942  3.13467  3.27956  4.36668  6.40902  3.92307      8 n - - E
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00341  6.07928  6.80162  0.61958  0.77255  0.44282  1.02784
+      7   3.32507  4.98102  3.78072  3.31043  2.85257  4.76439  5.09585  2.50332  4.69760  1.03851  3.36125  4.91001  2.73206  4.83820  4.72389  4.07376  3.83146  1.59790  5.60385  4.42704      9 l - - E
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.03752  6.08833  3.36505  0.61958  0.77255  0.48576  0.95510
+      8   3.15997  4.90658  3.35204  2.72775  4.53493  3.60960  2.65074  3.69535  2.11078  4.01384  4.99896  3.14668  4.61695  2.40643  2.34723  1.92358  2.03982  3.05153  6.39127  4.98082     10 s - - E
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00349  6.05430  6.77664  0.61958  0.77255  0.35749  1.20207
+      9   1.76295  3.98252  5.55061  4.93551  2.13202  3.39992  5.09294  2.14638  4.23898  2.23988  3.42109  4.92079  4.39252  3.70640  3.99349  3.50811  3.63432  1.47830  4.51148  4.41177     11 v - - E
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00338  6.08833  6.81068  0.61958  0.77255  0.48576  0.95510
+     10   3.01387  4.98892  2.91217  2.42744  5.22342  4.00576  3.74074  2.67275  2.47618  2.92529  3.89570  3.36720  4.15809  3.26810  2.80854  1.81572  2.02040  2.77133  4.92415  4.31555     12 s - - E
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00338  6.08833  6.81068  0.61958  0.77255  0.48576  0.95510
+     11   2.41247  5.98374  2.24093  2.04842  3.41543  2.59695  4.10033  4.81544  3.05501  4.28918  5.02429  2.22829  2.90635  3.12939  3.01921  2.37278  3.01194  3.02522  6.41619  3.66635     13 e - - E
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.06784  6.08833  2.75947  0.61958  0.77255  0.48576  0.95510
+     12   2.77725  4.36386  3.23435  2.92496  4.75140  4.31852  4.53101  1.91389  3.01135  2.51491  3.47932  2.97934  3.54432  2.88257  2.68923  3.07794  2.71169  1.80880  6.06849  4.75973     14 v - - E
+          2.68623  4.42259  2.77533  2.73059  3.46323  2.40500  3.72529  3.29333  2.67757  2.69369  4.24724  2.90364  2.73744  3.18108  2.89835  2.37891  2.77531  2.98493  4.58511  3.61510
+          0.22113  1.62346  6.74643  0.44471  1.02446  0.29166  1.37446
+     13   3.17575  5.97994  3.10322  2.84738  5.32369  2.00173  4.43389  4.80873  3.01150  3.75019  4.42663  2.23751  4.64014  2.74467  2.85546  1.99984  1.67133  4.36987  5.08444  3.58488     18 t - - C
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00338  6.08833  6.81068  0.61958  0.77255  0.48576  0.95510
+     14   2.14203  5.98483  2.53686  2.20884  5.33077  2.76253  3.61799  4.81737  2.91636  3.96256  5.02525  2.79307  2.44932  3.35978  3.34773  1.76758  2.51815  4.12754  4.53404  4.35768     19 s - - T
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.02274  6.08833  3.90154  0.61958  0.77255  0.48576  0.95510
+     15   3.45984  5.96297  2.32904  2.98671  5.30486  3.14893  3.59992  3.68067  2.95954  4.26690  5.00447  2.01875  4.62814  3.51950  2.89162  1.97303  1.47565  3.87160  6.39755  3.59993     20 t - - T
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00344  6.06904  6.79138  0.61958  0.77255  0.40302  1.10352
+     16   2.82603  5.98256  2.96292  2.53617  4.39559  3.14388  4.09532  4.81336  2.59005  4.28779  5.02326  3.12547  4.63955  2.76620  3.03618  1.28432  2.14874  3.55065  4.82032  3.29405     21 s - - E
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00338  6.08833  6.81068  0.61958  0.77255  0.48576  0.95510
+     17   2.29842  4.96481  5.56794  4.95172  2.45211  3.33868  4.31545  1.97312  4.73378  1.34355  2.88087  4.92903  5.12608  4.86259  4.73754  4.07438  3.55674  1.71344  5.58685  3.78328     22 l - - E
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00338  6.08833  6.81068  0.61958  0.77255  0.48576  0.95510
+     18   2.99930  4.68496  3.44656  2.53427  3.92510  4.04338  3.13178  3.10095  3.07007  2.68343  3.58599  3.17010  4.15335  2.63450  2.71950  2.30083  2.03779  2.23518  4.92400  3.84991     23 t - - E
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00338  6.08833  6.81068  0.61958  0.77255  0.48576  0.95510
+     19   3.61302  4.50726  5.99163  5.39935  2.74200  5.23506  5.61087  1.85210  5.20622  1.10188  3.56291  5.40353  5.56305  5.33364  5.22134  4.56441  3.85751  1.20867  6.05610  4.88933     24 l - - E
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00338  6.08833  6.81068  0.61958  0.77255  0.48576  0.95510
+     20   2.90508  5.98486  3.37356  2.37027  5.33083  3.46854  3.40789  4.81743  2.65230  3.22177  4.17825  2.67373  4.63906  2.52648  2.39431  1.50547  2.16764  4.37598  5.01440  5.00552     25 s - - E
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00338  6.08833  6.81068  0.61958  0.77255  0.48576  0.95510
+     21   5.54218  6.63564  6.83891  6.61797  2.57168  6.35073  5.30532  3.96643  6.37377  3.18917  5.26281  6.07009  4.35269  6.11992  6.21105  5.74680  5.75143  4.86346  0.24436  3.66807     26 W - - E
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00338  6.08833  6.81068  0.61958  0.77255  0.48576  0.95510
+     22   3.10862  5.98423  2.61761  2.10221  4.46995  3.93009  3.84182  3.79843  2.19229  3.09373  4.47555  2.66452  4.06864  2.59255  2.99987  1.99073  2.05618  3.67318  6.41655  4.47364     27 s - - E
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00338  6.08833  6.81068  0.61958  0.77255  0.48576  0.95510
+     23   2.05280  5.87614  3.77610  2.63103  5.17655  3.25143  3.55897  3.09279  2.68152  3.35866  4.92882  3.43937  1.44938  3.29932  2.98336  2.85751  2.78420  3.02863  4.43359  4.47040     28 p - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00338  6.08833  6.81068  0.61958  0.77255  0.48576  0.95510
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+          2.68557  4.42278  2.77404  2.73101  3.46370  2.40555  3.72548  3.29364  2.67779  2.69337  4.24743  2.90378  2.73741  3.18051  2.89835  2.37928  2.77557  2.98526  4.58530  3.61392
+          1.12909  0.74203  1.60680  0.24883  1.51281  1.67198  0.20810
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+          0.00508  5.68074  6.40309  0.61958  0.77255  0.20085  1.70396
+     28   2.96588  5.95917  2.45759  2.65943  5.30490  1.91234  3.11781  3.44164  2.78003  4.01788  4.99965  2.12379  3.26764  2.84040  2.87160  2.26272  3.15721  3.84740  4.86821  3.64128     35 g - - S
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
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+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
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+          0.00338  6.08833  6.81068  0.61958  0.77255  0.48576  0.95510
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+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
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+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
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+     43   2.89692  5.98568  2.39354  2.04021  5.33202  2.12548  3.27810  4.81889  2.36649  3.39071  4.58505  2.82477  4.63888  2.99231  3.02264  2.04514  2.45319  3.82791  6.41761  5.00590     53 e - - T
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
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+          2.68733  4.40831  2.77609  2.73043  3.46444  2.40393  3.72592  3.29278  2.67833  2.69426  4.24827  2.90407  2.73626  3.18024  2.89744  2.37952  2.77650  2.98614  4.58019  3.61570
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+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
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+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
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+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
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+          2.68571  4.42246  2.77540  2.73144  3.46375  2.40497  3.72515  3.29375  2.67742  2.69376  4.24711  2.90367  2.73710  3.18135  2.89822  2.37876  2.77540  2.98457  4.58498  3.61524
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+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
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+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00338  6.08833  6.81068  0.61958  0.77255  0.48576  0.95510
+     86   3.03720  5.94099  3.75455  2.96917  5.26587  2.91682  3.66571  4.11840  2.98472  4.23738  4.98891  3.74380  4.66031  3.40955  3.12788  0.72443  2.46104  4.32115  6.38683  4.99111    121 s - - E
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00227  6.08723        *  0.61958  0.77255  0.00000        *
+//
diff --git a/test/jalview/io/vcf/VCFLoaderTest.java b/test/jalview/io/vcf/VCFLoaderTest.java
index 7099282..7e3c0b4 100644
--- a/test/jalview/io/vcf/VCFLoaderTest.java
+++ b/test/jalview/io/vcf/VCFLoaderTest.java
@@ -577,7 +577,7 @@ public class VCFLoaderTest
     assertEquals(sf.getBegin(), 1);
     assertEquals(sf.getEnd(), 1);
     assertEquals(sf.getType(), SequenceOntologyI.SYNONYMOUS_VARIANT);
-    assertEquals(sf.getDescription(), "AGT");
+    assertEquals(sf.getDescription(), "agC/agT");
     sf = proteinFeatures.get(1);
     assertEquals(sf.getFeatureGroup(), "VCF");
     assertEquals(sf.getBegin(), 4);
diff --git a/test/jalview/renderer/OverviewResColourFinderTest.java b/test/jalview/renderer/OverviewResColourFinderTest.java
index 1687516..d01e53f 100644
--- a/test/jalview/renderer/OverviewResColourFinderTest.java
+++ b/test/jalview/renderer/OverviewResColourFinderTest.java
@@ -22,6 +22,7 @@ package jalview.renderer;
 
 import static org.testng.AssertJUnit.assertEquals;
 
+import jalview.api.AlignViewportI;
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
@@ -33,6 +34,7 @@ import jalview.gui.JvOptionPane;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.UserColourScheme;
 import jalview.schemes.ZappoColourScheme;
+import jalview.viewmodel.AlignmentViewport;
 
 import java.awt.Color;
 import java.util.ArrayList;
@@ -56,7 +58,7 @@ public class OverviewResColourFinderTest
   {
     SequenceI seq = new Sequence("name", "MA--TVLGSPRAPAFF");
     AlignmentI al = new Alignment(new SequenceI[] { seq });
-    final AlignViewport av = new AlignViewport(al);
+    final AlignViewportI av = new AlignViewport(al);
     ResidueColourFinder rcf = new OverviewResColourFinder();
 
     // gaps are grey, residues white
@@ -80,7 +82,7 @@ public class OverviewResColourFinderTest
     SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
                                                             // gap
     AlignmentI al = new Alignment(new SequenceI[] { seq });
-    final AlignViewport av = new AlignViewport(al);
+    final AlignViewportI av = new AlignViewport(al);
     ResidueColourFinder rcf = new OverviewResColourFinder();
     av.setGlobalColourScheme(new ZappoColourScheme());
 
@@ -126,7 +128,7 @@ public class OverviewResColourFinderTest
     SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
                                                             // gap
     AlignmentI al = new Alignment(new SequenceI[] { seq });
-    final AlignViewport av = new AlignViewport(al);
+    final AlignViewportI av = new AlignViewport(al);
     ResidueColourFinder rcf = new OverviewResColourFinder();
 
     Color[] newColours = new Color[24];
@@ -179,7 +181,7 @@ public class OverviewResColourFinderTest
     SequenceGroup[] groups = new SequenceGroup[1];
     groups[0] = sg;
     
-    final AlignViewport av = new AlignViewport(al);
+    final AlignViewportI av = new AlignViewport(al);
     ResidueColourFinder rcf = new OverviewResColourFinder();
     
     // G in group specified as magenta in Zappo
@@ -230,8 +232,6 @@ public class OverviewResColourFinderTest
   {
     SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
                                                             // gap
-    AlignmentI al = new Alignment(new SequenceI[] { seq });
-    final AlignViewport av = new AlignViewport(al);
 
     // non-legacy colouring
     ResidueColourFinder rcf = new OverviewResColourFinder();
@@ -269,9 +269,7 @@ public class OverviewResColourFinderTest
 
     // gaps gap colour
     c = rcf.getBoxColour(shader, seq, 3);
-    assertEquals(
-            jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP,
-            c);
+    assertEquals(OverviewResColourFinder.OVERVIEW_DEFAULT_GAP, c);
 
     // non legacy colouring with colour scheme
     rcf = new OverviewResColourFinder(false, Color.blue, Color.red);
diff --git a/test/jalview/renderer/ResidueColourFinderTest.java b/test/jalview/renderer/ResidueColourFinderTest.java
index 81fb2c0..24f653c 100644
--- a/test/jalview/renderer/ResidueColourFinderTest.java
+++ b/test/jalview/renderer/ResidueColourFinderTest.java
@@ -22,6 +22,7 @@ package jalview.renderer;
 
 import static org.testng.AssertJUnit.assertEquals;
 
+import jalview.api.AlignViewportI;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Sequence;
@@ -30,6 +31,7 @@ import jalview.gui.AlignViewport;
 import jalview.gui.JvOptionPane;
 import jalview.schemes.UserColourScheme;
 import jalview.schemes.ZappoColourScheme;
+import jalview.viewmodel.AlignmentViewport;
 
 import java.awt.Color;
 
@@ -51,7 +53,7 @@ public class ResidueColourFinderTest
   {
     SequenceI seq = new Sequence("name", "MATVLGSPRAPAFF"); // FER1_MAIZE...
     AlignmentI al = new Alignment(new SequenceI[] { seq });
-    final AlignViewport av = new AlignViewport(al);
+    final AlignViewportI av = new AlignViewport(al);
     ResidueColourFinder rcf = new ResidueColourFinder();
     av.setGlobalColourScheme(new ZappoColourScheme());
 
@@ -86,7 +88,7 @@ public class ResidueColourFinderTest
   {
     SequenceI seq = new Sequence("name", "MA--TVLGSPRAPAFF");
     AlignmentI al = new Alignment(new SequenceI[] { seq });
-    final AlignViewport av = new AlignViewport(al);
+    final AlignViewportI av = new AlignViewport(al);
     ResidueColourFinder rcf = new ResidueColourFinder();
 
     assertEquals(Color.white,
@@ -109,7 +111,7 @@ public class ResidueColourFinderTest
     SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
                                                             // gap
     AlignmentI al = new Alignment(new SequenceI[] { seq });
-    final AlignViewport av = new AlignViewport(al);
+    final AlignViewportI av = new AlignViewport(al);
     ResidueColourFinder rcf = new ResidueColourFinder();
 
     Color[] newColours = new Color[24];
diff --git a/test/jalview/renderer/ScaleRendererTest.java b/test/jalview/renderer/ScaleRendererTest.java
index 0af67cd..e78fc5a 100644
--- a/test/jalview/renderer/ScaleRendererTest.java
+++ b/test/jalview/renderer/ScaleRendererTest.java
@@ -6,10 +6,10 @@ import static org.testng.Assert.assertNull;
 import static org.testng.Assert.assertTrue;
 
 import jalview.gui.AlignFrame;
-import jalview.gui.AlignViewport;
 import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
 import jalview.renderer.ScaleRenderer.ScaleMark;
+import jalview.viewmodel.AlignmentViewport;
 
 import java.util.List;
 
@@ -23,7 +23,7 @@ public class ScaleRendererTest
     String data = ">Seq/20-45\nABCDEFGHIJKLMNOPQRSTUVWXYS\n";
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(data,
             DataSourceType.PASTE);
-    AlignViewport av = af.getViewport();
+    AlignmentViewport av = af.getViewport();
 
     /*
      * scale has minor ticks at 5, 15, 25, major at 10 and 20
diff --git a/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java b/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
index d8b905e..76e4fc5 100644
--- a/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
+++ b/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
@@ -6,11 +6,11 @@ import static org.testng.Assert.assertNotEquals;
 import static org.testng.Assert.assertNull;
 import static org.testng.Assert.assertTrue;
 
+import jalview.api.AlignViewportI;
 import jalview.api.FeatureColourI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
-import jalview.gui.AlignViewport;
 import jalview.gui.FeatureRenderer;
 import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
@@ -43,7 +43,7 @@ import org.testng.annotations.Test;
  */
 public class FeatureColourFinderTest
 {
-  private AlignViewport av;
+  private AlignViewportI av;
 
   private SequenceI seq;
 
diff --git a/test/jalview/schemes/ClustalxColourSchemeTest.java b/test/jalview/schemes/ClustalxColourSchemeTest.java
index d35ca76..af7036f 100644
--- a/test/jalview/schemes/ClustalxColourSchemeTest.java
+++ b/test/jalview/schemes/ClustalxColourSchemeTest.java
@@ -85,8 +85,6 @@ public class ClustalxColourSchemeTest
 
     // TODO more test cases; check if help documentation matches implementation
   }
-
-  // @formatter:on
   
   /**
    * Test for colour calculation when the consensus percentage ignores gapped
diff --git a/test/jalview/schemes/HmmerGlobalBackgroundTest.java b/test/jalview/schemes/HmmerGlobalBackgroundTest.java
new file mode 100644
index 0000000..13bf47b
--- /dev/null
+++ b/test/jalview/schemes/HmmerGlobalBackgroundTest.java
@@ -0,0 +1,91 @@
+package jalview.schemes;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.HMMFile;
+
+import java.awt.Color;
+import java.io.IOException;
+import java.net.MalformedURLException;
+
+import org.testng.annotations.Test;
+
+public class HmmerGlobalBackgroundTest {
+
+  @Test(groups = "Functional")
+  public void testFindColour() throws MalformedURLException, IOException
+  {
+    HMMFile file = new HMMFile("test/jalview/io/test_PKinase_hmm.txt",
+            DataSourceType.FILE);
+
+    SequenceI hmmSeq = file.getSeqsAsArray()[0];
+    AlignmentI al = new Alignment(new SequenceI[] { hmmSeq });
+    al.setHmmConsensus(hmmSeq);
+    ColourSchemeI scheme = new HmmerGlobalBackground(al);
+
+    /*
+     * 'A' in column 1, node 2, match emission 2.77204
+     * e-2.77204 = 0.0625 
+     * background frequency is 0.0826
+     * ratio is 0.757, log is negative, colour is Orange
+     */
+    Color actual = scheme.findColour('A', 1, null, null, 0);
+    assertEquals(actual, Color.ORANGE);
+
+    // gap is white
+    actual = scheme.findColour('-', 2, null, null, 0);
+    assertEquals(actual, Color.WHITE);
+    actual = scheme.findColour(' ', 2, null, null, 0);
+    assertEquals(actual, Color.WHITE);
+    actual = scheme.findColour('.', 2, null, null, 0);
+    assertEquals(actual, Color.WHITE);
+
+    /*
+     * 'Y' in column 4, node 5, match emission 4.41426
+     * e-4.41426 = 0.0121 
+     * background frequency is 0.0292
+     * ratio is 0.414, log is negative, colour is Orange
+     */
+    actual = scheme.findColour('Y', 4, null, null, 0);
+    assertEquals(actual, Color.ORANGE);
+
+    /*
+     * 'M' in column 109, no matching node, colour is reddish
+     */
+    actual = scheme.findColour('M', 109, null, null, 0);
+    assertEquals(actual, new Color(230, 0, 0));
+
+    /*
+     * 'I' in column 6, node 7, match emission 1.33015
+     * e-1.33015 = 0.2644
+     * background frequency is 0.0593
+     * ratio is 4.459, log is 1.495
+     * colour is graduated 1.495/4.52 or 84/255 of the way from
+     * white(255, 255, 255) to blue(0, 0, 255)
+     */
+    actual = scheme.findColour('I', 6, null, null, 0);
+    assertEquals(actual, new Color(171, 171, 255));
+
+    /*
+     * 'V' in column 14, node 15, match emission 0.44769
+     * e-0.44769 = 0.6391
+     * background frequency is 0.0686
+     * ratio is 9.316, log is 2.232
+     * colour is graduated 2.232/4.52 or 126/255 of the way from
+     * white(255, 255, 255) to blue(0, 0, 255)
+     */
+    actual = scheme.findColour('V', 14, null, null, 0);
+    assertEquals(actual, new Color(129, 129, 255));
+
+    /*
+     * invalid symbol is White
+     */
+    actual = scheme.findColour('X', 2, null, null, 0);
+    assertEquals(actual, Color.WHITE);
+  }
+
+}
diff --git a/test/jalview/schemes/HmmerLocalBackgroundTest.java b/test/jalview/schemes/HmmerLocalBackgroundTest.java
new file mode 100644
index 0000000..7467ab2
--- /dev/null
+++ b/test/jalview/schemes/HmmerLocalBackgroundTest.java
@@ -0,0 +1,78 @@
+package jalview.schemes;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.HMMFile;
+
+import java.awt.Color;
+import java.io.IOException;
+import java.net.MalformedURLException;
+
+import org.testng.annotations.Test;
+
+public class HmmerLocalBackgroundTest {
+
+  @Test(groups = "Functional")
+  public void testFindColour() throws MalformedURLException, IOException
+  {
+    HMMFile file = new HMMFile("test/jalview/io/test_PKinase_hmm.txt",
+            DataSourceType.FILE);
+
+    /*
+     * alignment with 20 residues and background frequencies:
+     * A/a, S 3/20 = 0.15
+     * M, K 4/20 = 0.2
+     * V 2/20 = 0.1
+     * Q, R, L 1/20 = 0.05
+     * log(totalCount) = log(20) = 2.996
+     */
+    SequenceI seq1 = new Sequence("seq1", "AAMMMKKKVV");
+    SequenceI seq2 = new Sequence("seq2", "aAM-QKRSSSL");
+    SequenceI hmmSeq = file.getSeqsAsArray()[0];
+    AnnotatedCollectionI ac = new Alignment(
+            new SequenceI[]
+            { hmmSeq, seq1, seq2 });
+    ac.setHmmConsensus(hmmSeq);
+    ColourSchemeI scheme = new HmmerLocalBackground(ac);
+
+    /*
+     * 'A' in column 1, node 2, match emission 2.77204
+     * e-2.77204 = 0.0625 
+     * background frequency is 0.15
+     * ratio is < 1, log is negative, colour is Orange
+     */
+    Color actual = scheme.findColour('A', 1, null, null, 0);
+    assertEquals(actual, Color.ORANGE);
+
+    // gap is white
+    actual = scheme.findColour('-', 2, null, null, 0);
+    assertEquals(actual, Color.WHITE);
+    actual = scheme.findColour(' ', 2, null, null, 0);
+    assertEquals(actual, Color.WHITE);
+    actual = scheme.findColour('.', 2, null, null, 0);
+    assertEquals(actual, Color.WHITE);
+
+    /*
+     * 'L' in column 3, node 4, match emission 1.98342
+     * e-1.98342 = 0.1376 
+     * background frequency is 0.05
+     * ratio is 2.752, log is 1.012
+     * colour is graduated 1.012/2.996 or 86/255 of the way from
+     * white(255, 255, 255) to blue(0, 0, 255)
+     */
+    actual = scheme.findColour('L', 3, null, null, 0);
+    assertEquals(actual, new Color(169, 169, 255));
+
+    /*
+     * invalid symbol is White
+     */
+    actual = scheme.findColour('X', 2, null, null, 0);
+    assertEquals(actual, Color.WHITE);
+  }
+
+}
diff --git a/test/jalview/schemes/PIDColourSchemeTest.java b/test/jalview/schemes/PIDColourSchemeTest.java
index fa4b5d9..c2f86d6 100644
--- a/test/jalview/schemes/PIDColourSchemeTest.java
+++ b/test/jalview/schemes/PIDColourSchemeTest.java
@@ -4,9 +4,9 @@ import static org.testng.Assert.assertEquals;
 
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
-import jalview.gui.AlignViewport;
 import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
+import jalview.viewmodel.AlignmentViewport;
 
 import java.awt.Color;
 
@@ -83,7 +83,7 @@ public class PIDColourSchemeTest
      */
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqs,
             DataSourceType.PASTE);
-    AlignViewport viewport = af.getViewport();
+    AlignmentViewport viewport = af.getViewport();
     viewport.setIgnoreGapsConsensus(false, af.alignPanel);
     while (viewport.getConsensusSeq() == null)
     {
diff --git a/test/jalview/structure/StructureSelectionManagerTest.java b/test/jalview/structure/StructureSelectionManagerTest.java
index a59fbde..286be1b 100644
--- a/test/jalview/structure/StructureSelectionManagerTest.java
+++ b/test/jalview/structure/StructureSelectionManagerTest.java
@@ -20,28 +20,53 @@
  */
 package jalview.structure;
 
+import static org.junit.Assert.assertArrayEquals;
+import static org.testng.Assert.assertNotNull;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.analysis.AlignmentUtils;
+import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.bin.Cache;
 import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.ext.jmol.JmolCommands;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
 import jalview.gui.JvOptionPane;
+import jalview.gui.SequenceRenderer;
+import jalview.gui.StructureChooser;
 import jalview.io.DataSourceType;
+import jalview.io.FileLoader;
+import jalview.io.Jalview2xmlBase;
 import jalview.io.StructureFile;
 import jalview.util.MapList;
+import jalview.ws.DBRefFetcher;
+import jalview.ws.sifts.SiftsSettings;
 
 import java.util.ArrayList;
+import java.util.LinkedHashMap;
 import java.util.List;
+import java.util.Map;
+import java.util.SortedMap;
+import java.util.TreeMap;
 
+import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
-public class StructureSelectionManagerTest
+@Test(singleThreaded = true)
+public class StructureSelectionManagerTest extends Jalview2xmlBase
 {
 
+  @Override
   @BeforeClass(alwaysRun = true)
   public void setUpJvOptionPane()
   {
@@ -160,4 +185,313 @@ public class StructureSelectionManagerTest
     assertEquals("1gaq", sf.getFeatureGroup());
     assertEquals("ALA:   1  1gaqB", sf.getDescription());
   }
+
+  /**
+   * Verify that RESNUM sequence features are present after creating a PDB
+   * mapping from a local file, then that everything stays in the same place
+   * when the file is viewed. The corner case is that 4IM2 is a fragment of a
+   * PDB file, which still includes the 'ID' field - a bug in Jalview 2.10.3
+   * causes features, annotation and positions to be remapped to the wrong place
+   * on viewing the structure
+   */
+  @Test(groups = { "Network" })
+  public void testMapping_EqualsFeatures()
+  {
+    // for some reason 'BeforeMethod' (which should be inherited from
+    // Jalview2XmlBase isn't always called)...
+    Desktop.instance.closeAll_actionPerformed(null);
+    try { 
+      Thread.sleep(200);
+    } catch (Exception foo) {}; 
+    SequenceI seq = new Sequence("4IM2|A",
+            "LDFCIRNIEKTVMGEISDIHTKLLRLSSSQGTIE");
+    String P4IM2_MISSING = "examples/testdata/4IM2_missing.pdb";
+    StructureSelectionManager sm = new StructureSelectionManager();
+    sm.setProcessSecondaryStructure(true);
+    sm.setAddTempFacAnnot(true);
+    StructureFile pmap = sm.setMapping(true, new SequenceI[] { seq },
+            new String[]
+            { null }, P4IM2_MISSING,
+            DataSourceType.FILE);
+    assertTrue(pmap != null);
+
+    assertEquals(1, pmap.getSeqs().size());
+    assertEquals("4IM2|A", pmap.getSeqs().get(0).getName());
+
+    List<int[]> structuremap1 = new ArrayList(
+            sm.getMapping(P4IM2_MISSING)[0]
+                    .getPDBResNumRanges(seq.getStart(), seq.getEnd()));
+
+    /*
+     * Verify a RESNUM sequence feature in the PDBfile sequence
+     * LEU468 - start+0 
+     * VAL479 - start+11
+     * MET486 - start+12
+     * GLY496 - start+13
+     * GLU516 - start+33 (last)
+     * 
+     * Expect features and mapping to resolve to same residues.
+     * Also try creating a view and test again
+     *   
+     */
+    String[] feats = new String[] { "LEU", "468", "VAL", "479", "MET",
+        "486", "GLY", "496", "GLU", "516" };
+    int[] offset = new int[] { 0, 11, 12, 13, 33 };
+
+    List<String> fdesc = new ArrayList<>();
+    for (int f = 0; f < feats.length; f += 2)
+    {
+      fdesc.add(feats[f] + ": " + feats[f + 1] + "  4im2A");
+    }
+    SequenceI pdbseq = pmap.getSeqs().get(0);
+    verifySeqFeats(pdbseq, offset, fdesc);
+
+    /// Now load as a view
+
+    AlignFrame alf = new FileLoader(false).LoadFileWaitTillLoaded(
+            "examples/testdata/4IM2_missing.pdb", DataSourceType.FILE);
+    Desktop.addInternalFrame(alf, "examples/testdata/4IM2_missing.pdb", 800,
+            400);
+    AlignmentI pdbal = alf.getViewport().getAlignment();
+    SequenceI pdb_viewseq = pdbal.getSequenceAt(0);
+    assertEquals(pdb_viewseq.getSequenceAsString(),
+            seq.getSequenceAsString());
+    // verify the feature location on the sequence when pdb imported as an
+    // alignment
+    verifySeqFeats(pdb_viewseq, offset, fdesc);
+
+
+    JalviewStructureDisplayI viewr = openStructureViaChooser(alf,
+            pdb_viewseq, "4IM2");
+
+    // and check all is good with feature location still
+    verifySeqFeats(pdb_viewseq, offset, fdesc);
+
+    // finally check positional mapping for sequence and structure
+    PDBEntry pdbe = seq.getPDBEntry("4IM2");
+    StructureSelectionManager apssm = alf.alignPanel
+            .getStructureSelectionManager();
+    StructureMapping[] smap = apssm
+            .getMapping(pdbe.getFile());
+    assertNotNull(smap);
+    assertNotNull(smap[0]);
+    // find the last position in the alignment sequence - this is not
+    // 'SequenceI.getEnd()' - which gets the last PDBRESNUM rather than
+    // SequenceI.getStart() + number of residues in file...
+    int realSeqEnd = pdb_viewseq.findPosition(pdb_viewseq.getLength());
+    List<int[]> ranges = smap[0].getPDBResNumRanges(pdb_viewseq.getStart(),
+            realSeqEnd);
+    assertEquals(structuremap1.size(), ranges.size());
+    int tot_mapped = 0;
+    for (int p = 0; p < ranges.size(); p++)
+    {
+      assertArrayEquals(structuremap1.get(p), ranges.get(p));
+      tot_mapped += 1 + (structuremap1.get(p)[1] - structuremap1.get(p)[0]);
+    }
+
+    assertEquals(pdb_viewseq.getLength(), tot_mapped);
+
+    int lastmappedp = StructureMapping.UNASSIGNED_VALUE;
+    for (int rp = pdb_viewseq.getStart(), rpEnd = pdb_viewseq
+            .findPosition(pdb_viewseq.getLength() - 1); rp <= rpEnd; rp++)
+    {
+      int mappedp = smap[0].getPDBResNum(rp);
+      if (mappedp != StructureMapping.UNASSIGNED_VALUE)
+      {
+        tot_mapped--;
+        if (lastmappedp == mappedp)
+        {
+          Assert.fail("Duplicate mapped position at " + rp + " (dupe = "
+                  + mappedp + ")");
+        }
+      }
+    }
+
+    Assert.assertEquals(tot_mapped, 0,
+            "Different number of mapped residues compared to ranges of mapped residues");
+
+    // positional mapping to atoms for color by structure is still wrong, even
+    // though panel looks correct.
+
+    StructureMappingcommandSet smcr[] = JmolCommands
+            .getColourBySequenceCommand(apssm,
+            new String[]
+            { pdbe.getFile() },
+            new SequenceI[][]
+            { new SequenceI[] { pdb_viewseq } },
+                    new SequenceRenderer(alf.alignPanel.getAlignViewport()),
+                    alf.alignPanel);
+    // Expected - all residues are white
+    for (StructureMappingcommandSet smm : smcr)
+    {
+      for (String c : smm.commands)
+      {
+        System.out.println(c);
+      }
+    }
+  }
+
+  private void verifySeqFeats(SequenceI pdbseq, int[] offset,
+          List<String> fdesc)
+  {
+    for (int o = 0; o < offset.length; o++)
+    {
+      int res = pdbseq.findPosition(offset[o]);
+      List<SequenceFeature> sf = pdbseq.getFeatures().findFeatures(res, res,
+              "RESNUM");
+      assertEquals("Expected sequence feature at position " + res + "("
+              + offset[o] + ")", 1, sf.size());
+      assertEquals("Wrong description at " + res + "(" + offset[o] + ")",
+              fdesc.get(o), sf.get(0).getDescription());
+    }
+
+  }
+
+  @Test(groups = { "Network" })
+  public void testAssociatedMappingToSubSeq() throws Exception
+  {
+
+    // currently this test fails if trimming is enabled
+    Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
+            Boolean.FALSE.toString());
+    String TEMP_FACTOR_AA="Temperature Factor";
+    String PDBID = "4IM2";
+    String FullLengthSeq = ">TBK1_HUMAN Serine/threonine-protein kinase TBK1\n" + 
+            "MQSTSNHLWLLSDILGQGATANVFRGRHKKTGDLFAIKVFNNISFLRPVDVQMREFEVLKKLNHKNIVKLFA\n" + 
+            "IEEETTTRHKVLIMEFCPCGSLYTVLEEPSNAYGLPESEFLIVLRDVVGGMNHLRENGIVHRDIKPGNIMRV\n" + 
+            "IGEDGQSVYKLTDFGAARELEDDEQFVSLYGTEEYLHPDMYERAVLRKDHQKKYGATVDLWSIGVTFYHAAT\n" + 
+            "GSLPFRPFEGPRRNKEVMYKIITGKPSGAISGVQKAENGPIDWSGDMPVSCSLSRGLQVLLTPVLANILEAD\n" + 
+            "QEKCWGFDQFFAETSDILHRMVIHVFSLQQMTAHKIYIHSYNTATIFHELVYKQTKIISSNQELIYEGRRLV\n" + 
+            "LEPGRLAQHFPKTTEENPIFVVSREPLNTIGLIYEKISLPKVHPRYDLDGDASMAKAITGVVCYACRIASTL\n" + 
+            "LLYQELMRKGIRWLIELIKDDYNETVHKKTEVVITLDFCIRNIEKTVKVYEKLMKINLEAAELGEISDIHTK\n" + 
+            "LLRLSSSQGTIETSLQDIDSRLSPGGSLADAWAHQEGTHPKDRNVEKLQVLLNCMTEIYYQFKKDKAERRLA\n" + 
+            "YNEEQIHKFDKQKLYYHATKAMTHFTDECVKKYEAFLNKSEEWIRKMLHLRKQLLSLTNQCFDIEEEVSKYQ\n" + 
+            "EYTNELQETLPQKMFTASSGIKHTMTPIYPSSNTLVEMTLGMKKLKEEMEGVVKELAENNHILERFGSLTMD\n" + 
+            "GGLRNVDCL";
+    /*
+     * annotation exported after importing full length sequence to desktop, opening 4IM2 and selecting 'Add Reference Annotation'.
+     * 
+     * Note - tabs must be replaced with \t - Eclipse expands them to spaces otherwise.
+     */
+    String FullLengthAnnot = "JALVIEW_ANNOTATION\n" + 
+            "# Created: Mon Feb 05 15:30:20 GMT 2018\n" + 
+            "# Updated: Fri Feb 09 17:05:17 GMT 2018\n" + 
+            "\n" + 
+            "\n" + 
+            "SEQUENCE_REF\tTBK1_HUMAN\n"
+            + "LINE_GRAPH\tTemperature Factor\tTemperature Factor for 4im2A\t125.22|128.51|120.35|113.12|122.6|114.44|91.49|102.53|98.22|111.41|111.32|116.64|103.55|100.53|95.07|105.55|114.76|128.29|133.55|142.14|121.12|110.36|95.79|95.39|87.14|99.56|93.55|94.21|100.33|110.68|97.85|82.37|75.87|76.53|77.85|82.49|80.92|96.88|122.58|133.31|160.15|180.51|||||242.88|258.97|247.01|227.12|223.24|211.62|184.65|183.51|168.96|160.04|150.88|131.68|130.43|139.87|148.59|136.57|125.7|96.51|74.49|74.08|85.87|70.93|86.47|101.59|97.51|97.39|117.19|114.27|129.5|112.98|147.52|170.26|154.98|168.18|157.51|131.95|105.85|97.78|97.35|76.51|76.31|72.55|71.43|78.82|79.94|75.04|79.54|77.95|83.56|88.5|71.51|71.73|75.96|82.36|81.75|66.51|67.23|69.35|67.92|54.75|71.19|61.85|65.34|67.97|64.51|67.41|62.28|72.85|72.76|70.64|65.23|71.07|67.73|87.72|64.93|75.92|94.02|99.35|93.71|103.59|106.29|115.46|118.69|147.18|130.62|171.64|158.95|164.11||107.42|88.53|83.52|88.06|94.06|80.82|59.01|59.73|78.89|69.21|70.34|81.95|74.53|60.92|64.65|55.79|75.71|68.86|70.95|75.08|87.76|85.43|105.84|||||||||||||||||137.46|151.33|145.17|122.79|111.56|126.72|124.06|161.75|176.84|180.51|198.49|196.75|187.41||195.23|202.27|203.16|226.55|221.75|193.83||||||172.33|177.97|151.47|132.65|99.22|93.7|91.15|88.24|72.35|70.05|70.0|74.92|66.51|68.37|65.76|70.12|74.97|76.89|80.83|70.21|69.48|79.54|82.65|96.54|114.31|140.46|168.51|176.99|205.08|209.27|155.83|139.41|151.3|129.33|111.31|119.62|121.37|102.26|115.39|129.97|128.65|110.38|110.66|116.1|82.53|84.02|82.17|87.63|86.42|77.23|91.23|95.53|102.21|120.73|133.26|109.67|108.49|93.25|92.85|86.39|95.66|94.92|85.82|80.13|76.17|86.61|78.9|77.97|105.6|70.66|69.35|78.94|66.68|63.03|69.91|79.05|75.43|70.73|70.02|80.57|81.74|77.99|84.1|91.66|92.42|94.03|116.47|132.01|154.55|163.99|161.37|155.23|132.78|109.3|90.38|101.83|99.61|91.68|82.77|86.12|82.73|90.13|85.14|79.54|74.27|74.06|72.88|86.34|72.0|69.32|60.9|68.15|52.99|63.53|61.3|66.01|68.28|77.41|71.52|67.18|66.17|71.51|65.47|52.63|65.08|66.37|73.76|77.79|67.58|79.53|84.75|87.42|78.9|79.19|85.57|73.67|80.56|86.19|72.17|66.27|72.8|86.28|78.89|74.5|90.6|80.42|92.5|92.84|96.18|92.08|88.5|87.25|64.6|68.95|65.56|67.55|71.62|78.24|84.95|71.35|86.41|84.73|94.41|95.09|84.74|87.64|88.85|75.1|86.42|79.28|73.14|78.54|80.81|60.66|67.93|71.64|59.85|64.7|61.22|63.84|65.9|62.18|74.95|72.92|93.37|90.47|96.0|93.8|88.46|79.78|83.4|66.55|68.7|73.2|78.76|85.67|84.8|89.59|96.52|79.53|103.51|134.72|126.7|145.31|156.17|149.35|128.48|117.29|118.98|131.59|109.36|90.39|87.68|91.81|78.77|80.11|91.39|75.57|78.98|71.53|76.85|70.9|64.71|73.55|73.45|60.0|69.92|57.89|69.07|66.45|62.85|57.83|57.89|66.4|61.61|60.85|66.47|63.53|63.84|65.96|73.06|70.82|64.51|63.66|73.37|73.59|68.09|78.93|76.99|75.05|71.32|88.4|78.88|93.08|110.61|94.32|99.24|128.99|129.49|132.74|124.21|120.32|142.06|166.41|149.87|153.29|172.19|165.89|181.6|223.11|237.73|176.41|171.09|189.65|188.61|154.84|142.72|154.25|170.99|175.65|||||||110.61||||||||||158.07|170.73|167.93|198.47|212.36|181.71|157.69|163.31|138.96|120.29|131.63|152.26|125.06|136.66|148.97|129.68|120.52|135.31|136.05|119.39|124.18|128.94|123.02|103.37|128.44|134.12|118.88|120.94|130.38|124.67|112.21|113.69|123.65|132.06|114.97|110.75|92.38|101.2|103.25|94.84|85.3|82.19|89.81|98.81|83.03|68.91|65.24|70.31|63.49|86.38|71.07|62.65|63.95|66.98|58.06|68.28|62.11|63.86|67.4|68.69|69.57|68.03|74.23|75.66|70.67|81.08|81.31|82.49|88.15|95.99|92.97|100.01|113.18|122.37|110.99|122.19|159.27|147.74|133.96|111.2|115.64|126.55|107.15|102.85|117.06|116.56|109.55|96.82|98.92|96.53|86.0|88.11|92.76|85.77|79.41|93.06|86.96|76.35|72.37|74.19|68.6|67.46|74.47|76.25|66.73|73.18|75.2|88.21|84.93|75.04|71.09|82.6|80.03|76.22|75.76|83.72|75.85|79.36|90.35|86.9|78.24|95.64|97.38|86.41|85.02|91.87|87.36|77.56|81.25|91.66|83.65|77.67|85.07|89.21|92.66|92.46|89.0|100.83|96.71|94.81|101.37|111.28|124.48|119.73|127.81|134.41|132.4|140.32|140.86|166.52|160.16|168.39|176.74|174.63|172.86|168.55|155.9|132.71|113.44|113.49|123.9|151.11|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n"
+            + 
+            "\n" + 
+            "";
+    AlignFrame alf_full=new
+     FileLoader(false).LoadFileWaitTillLoaded(FullLengthSeq,DataSourceType.PASTE);
+    alf_full.loadJalviewDataFile(FullLengthAnnot, DataSourceType.PASTE, null, null);
+    AlignmentI al_full = alf_full.getViewport().getAlignment();
+    AlignmentAnnotation fullseq_tf = al_full.findAnnotations(al_full.getSequences().get(0), null, TEMP_FACTOR_AA).iterator()
+            .next();
+    assertNotNull(fullseq_tf);
+    
+    // getMappingFor
+    // AlignmentI al_full=alf_full.getViewport().getAlignment();
+    //
+    // // load 4IM2 (full length, SIFTS onto full alingnment)
+    // SiftsSettings.setMapWithSifts(true);
+    // StructureChooser schoose = new StructureChooser(selectedSeqs_full,
+    // seq_full,
+    // alf_full.getViewport().getAlignPanel());
+    // schoose.selectStructure(PDBID);
+    // schoose.ok_ActionPerformed();
+
+    AlignFrame alf = new FileLoader(false).LoadFileWaitTillLoaded(
+            ">TBK1_HUMAN/470-502 Serine/threonine-protein kinase TBK1\nFCIRNIEKTVKVYEKLMKINLEAAELGEISDIH",
+            DataSourceType.PASTE);
+    Desktop.addInternalFrame(alf, "Foo", 800, 600);
+    ;
+    AlignmentI al = alf.getViewport().getAlignment();
+    SequenceI seq = al.getSequenceAt(0);
+    assertEquals(470, seq.getStart());
+    // load 4IM2 (full length, SIFTS)
+    SiftsSettings.setMapWithSifts(true);
+    StructureImportSettings.setProcessSecondaryStructure(true);
+    StructureImportSettings.setVisibleChainAnnotation(true);
+    JalviewStructureDisplayI sview = openStructureViaChooser(alf, seq,
+            PDBID);
+
+    AlignmentAnnotation subseq_tf=null;
+    assertTrue(seq.getDBRefs() != null && seq.getDBRefs().length > 0);
+    
+    if (!al.findAnnotations(seq, null, TEMP_FACTOR_AA).iterator().hasNext())
+    {
+      // FIXME JAL-2321 - don't see reference annotation on alignment the first
+      // time
+      // around
+      SortedMap<String, String> tipEntries = new TreeMap<>();
+      final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
+
+      AlignmentUtils.findAddableReferenceAnnotations(al.getSequences(),
+              tipEntries, candidates, al);
+      AlignmentUtils.addReferenceAnnotations(candidates, al, null);
+
+      if (!al.findAnnotations(seq, null, TEMP_FACTOR_AA).iterator()
+              .hasNext())
+      {
+        Assert.fail(
+                "JAL-2321 or worse has occured. No secondary structure added to alignment.");
+      }
+    }
+    subseq_tf = al.findAnnotations(seq, null, TEMP_FACTOR_AA).iterator()
+            .next();
+    // verify against annotation after loading 4IM2 to full length TBK1_HUMAN
+    // verify location of mapped residues
+    // verify location of secondary structure annotation
+    // Specific positions: LYS477 (h),THR478 (no helix), ... GLY496(no helix),
+    // GLU497 (helix),
+    
+    // check there is or is not a tempfactor for each mapped position, and that
+    // values are equal for those positions.
+    for (int p=seq.getStart();p<=seq.getEnd();p++)
+    {
+      Annotation orig,subseq;
+      orig = fullseq_tf.getAnnotationForPosition(p);
+      subseq = subseq_tf.getAnnotationForPosition(p);
+      if (orig == null)
+      {
+        Assert.assertNull(subseq,
+                "Expected no annotation transferred at position " + p);
+      }
+      ;
+      if (orig != null)
+      {
+        Assert.assertNotNull(subseq,
+                "Expected annotation transfer at position " + p);
+        assertEquals(orig.value, subseq.value);
+      }
+      ;
+
+    }
+  }
+
+  private JalviewStructureDisplayI openStructureViaChooser(AlignFrame alf,
+          SequenceI seq,
+          String pDBID)
+  {
+
+    SequenceI[] selectedSeqs = new SequenceI[] { seq };
+
+    StructureChooser schoose = new StructureChooser(selectedSeqs, seq,
+            alf.getViewport().getAlignPanel());
+
+    try
+    {
+      Thread.sleep(5000);
+    } catch (InterruptedException q)
+    {
+    }
+    ;
+    Assert.assertTrue(schoose.selectStructure(pDBID),
+            "Couldn't select structure via structure chooser: " + pDBID);
+    schoose.showStructures(true);
+    return schoose.getOpenedStructureViewer();
+  }
+
 }
diff --git a/test/jalview/util/Binned.csv b/test/jalview/util/Binned.csv
new file mode 100644
index 0000000..f140646
--- /dev/null
+++ b/test/jalview/util/Binned.csv
@@ -0,0 +1,4 @@
+1.8, 4.53
+3.4, 2.65
+0, 5.4
+6.4, 10.8
\ No newline at end of file
diff --git a/test/jalview/util/HMMProbabilityDistributionAnalyserTest.java b/test/jalview/util/HMMProbabilityDistributionAnalyserTest.java
new file mode 100644
index 0000000..4dbf05e
--- /dev/null
+++ b/test/jalview/util/HMMProbabilityDistributionAnalyserTest.java
@@ -0,0 +1,119 @@
+package jalview.util;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertNull;
+
+import jalview.datamodel.HMMNode;
+import jalview.datamodel.HiddenMarkovModel;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.Vector;
+
+import org.testng.annotations.Test;
+
+import junit.extensions.PA;
+
+public class HMMProbabilityDistributionAnalyserTest {
+
+  HMMProbabilityDistributionAnalyser analyser = new HMMProbabilityDistributionAnalyser();
+
+  @Test
+  public void testMoveToFile() throws IOException
+  {
+
+    BufferedReader br = new BufferedReader(new FileReader(
+            "test/jalview/util/test_Fams_for_probability_analysis"));
+    analyser.moveLocationBy(1, br);
+
+    String line = br.readLine();
+    assertEquals(line, "# STOCKHOLM 1.0");
+    line = br.readLine();
+    assertEquals(line, "seq1 ATW");
+    line = br.readLine();
+    assertEquals(line, "seq2 ATI");
+
+  }
+
+  @Test
+  public void testCountValidResidues()
+  {
+    analyser.sequences = new Vector<>();
+    analyser.hmm = new HiddenMarkovModel();
+    analyser.hmm.setProperty("LENG", "8");
+
+    List<HMMNode> nodes = new ArrayList<>();
+    nodes.add(new HMMNode());
+    for (int i = 1; i < 9; i++)
+    {
+      HMMNode node = new HMMNode();
+      node.setResidueNumber(i - 1);
+      nodes.add(node);
+
+    }
+    PA.setValue(analyser.hmm, "nodes", nodes);
+
+    SequenceI[] sequence = new Sequence[] {
+        new Sequence("seq1", "ATGWWSCF"), new Sequence("seq2", "GGMKI"),
+        new Sequence("seq3", "--.ATccGc") };
+    analyser.sequences.add(sequence[0]);
+    analyser.sequences.add(sequence[1]);
+    analyser.sequences.add(sequence[2]);
+
+    int count = analyser.countValidResidues();
+    assertEquals(count, 16);
+  }
+
+  @Test(priority = 0)
+  public void testReadBinned() throws IOException
+  {
+    analyser.readBinned("test/jalview/util/");
+    Map<String, Double> map = analyser.binned;
+    assertEquals(map.get("1.8"), 4.53);
+    assertEquals(map.get("3.4"), 2.65);
+    assertEquals(map.get("6.4"), 10.8);
+    assertEquals(map.get("0"), 5.4);
+  }
+
+  @Test
+  public void testReadRaw() throws IOException
+  {
+    analyser.readRaw("test/jalview/util/");
+    List<ArrayList<Double>> list = analyser.raw;
+
+    assertEquals(list.get(0).get(0), 1.43);
+    assertNull(list.get(0).get(2));
+    assertEquals(list.get(1).get(1), 1.2);
+    assertEquals(list.get(2).get(0), 5.6);
+    assertEquals(list.get(2).get(2), 6.8);
+
+  }
+
+  @Test(priority = 1)
+  public void testProcessData() throws IOException
+  {
+    analyser.keepRaw = true;
+    BufferedReader brFam = new BufferedReader(new FileReader(
+            "test/jalview/util/test_Fams_for_probability_analysis"));
+    BufferedReader brHMM = new BufferedReader(new FileReader(
+            "test/jalview/util/test_HMMs_for_probability_analysis"));
+    analyser.readStockholm(brFam);
+    analyser.readHMM(brHMM);
+    analyser.processData(6);
+    Map<String, Double> map = analyser.binned;
+    List<ArrayList<Double>> list = analyser.raw;
+    assertEquals(map.get("1.8"), 4.863, 0.001d);
+    assertEquals(map.get("3.4"), 2.65);
+    assertEquals(map.get("0"), 5.4);
+    assertEquals(map.get("6.4"), 10.8);
+    assertEquals(map.get("1.4"), 0.166667, 0.00001d);
+    assertEquals(map.get("4.4"), 0.5);
+
+  }
+}
diff --git a/test/jalview/util/MapListTest.java b/test/jalview/util/MapListTest.java
index 029b681..fd68e96 100644
--- a/test/jalview/util/MapListTest.java
+++ b/test/jalview/util/MapListTest.java
@@ -599,60 +599,6 @@ public class MapListTest
     assertEquals("[ [11, 16] ] 1:3 to [ [72, 53] ]", ml.toString());
   }
 
-  @Test(groups = "Functional")
-  public void testAddRange()
-  {
-    int[] range = { 1, 5 };
-    List<int[]> ranges = new ArrayList<>();
-
-    // add to empty list:
-    MapList.addRange(range, ranges);
-    assertEquals(1, ranges.size());
-    assertSame(range, ranges.get(0));
-
-    // extend contiguous (same position):
-    MapList.addRange(new int[] { 5, 10 }, ranges);
-    assertEquals(1, ranges.size());
-    assertEquals(1, ranges.get(0)[0]);
-    assertEquals(10, ranges.get(0)[1]);
-
-    // extend contiguous (next position):
-    MapList.addRange(new int[] { 11, 15 }, ranges);
-    assertEquals(1, ranges.size());
-    assertEquals(1, ranges.get(0)[0]);
-    assertEquals(15, ranges.get(0)[1]);
-
-    // change direction: range is not merged:
-    MapList.addRange(new int[] { 16, 10 }, ranges);
-    assertEquals(2, ranges.size());
-    assertEquals(16, ranges.get(1)[0]);
-    assertEquals(10, ranges.get(1)[1]);
-
-    // extend reverse contiguous (same position):
-    MapList.addRange(new int[] { 10, 8 }, ranges);
-    assertEquals(2, ranges.size());
-    assertEquals(16, ranges.get(1)[0]);
-    assertEquals(8, ranges.get(1)[1]);
-
-    // extend reverse contiguous (next position):
-    MapList.addRange(new int[] { 7, 6 }, ranges);
-    assertEquals(2, ranges.size());
-    assertEquals(16, ranges.get(1)[0]);
-    assertEquals(6, ranges.get(1)[1]);
-
-    // change direction: range is not merged:
-    MapList.addRange(new int[] { 6, 9 }, ranges);
-    assertEquals(3, ranges.size());
-    assertEquals(6, ranges.get(2)[0]);
-    assertEquals(9, ranges.get(2)[1]);
-
-    // not contiguous: not merged
-    MapList.addRange(new int[] { 11, 12 }, ranges);
-    assertEquals(4, ranges.size());
-    assertEquals(11, ranges.get(3)[0]);
-    assertEquals(12, ranges.get(3)[1]);
-  }
-
   /**
    * Check state after construction
    */
diff --git a/test/jalview/util/MappingUtilsTest.java b/test/jalview/util/MappingUtilsTest.java
index d4cf98a..af82ac6 100644
--- a/test/jalview/util/MappingUtilsTest.java
+++ b/test/jalview/util/MappingUtilsTest.java
@@ -50,6 +50,7 @@ import java.awt.Color;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Iterator;
 import java.util.List;
 
 import org.testng.annotations.BeforeClass;
@@ -913,9 +914,9 @@ public class MappingUtilsTest
     MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
             proteinView, dnaView, dnaSelection, dnaHidden);
     assertEquals("[]", dnaSelection.getSelected().toString());
-    List<int[]> hidden = dnaHidden.getHiddenColumnsCopy();
-    assertEquals(1, hidden.size());
-    assertEquals("[0, 4]", Arrays.toString(hidden.get(0)));
+    Iterator<int[]> regions = dnaHidden.iterator();
+    assertEquals(1, dnaHidden.getNumberOfRegions());
+    assertEquals("[0, 4]", Arrays.toString(regions.next()));
 
     /*
      * Column 1 in protein picks up Seq1/K which maps to cols 0-3 in dna
@@ -930,9 +931,9 @@ public class MappingUtilsTest
     proteinSelection.hideSelectedColumns(1, hiddenCols);
     MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
             proteinView, dnaView, dnaSelection, dnaHidden);
-    hidden = dnaHidden.getHiddenColumnsCopy();
-    assertEquals(1, hidden.size());
-    assertEquals("[0, 3]", Arrays.toString(hidden.get(0)));
+    regions = dnaHidden.iterator();
+    assertEquals(1, dnaHidden.getNumberOfRegions());
+    assertEquals("[0, 3]", Arrays.toString(regions.next()));
 
     /*
      * Column 2 in protein picks up gaps only - no mapping
@@ -944,7 +945,7 @@ public class MappingUtilsTest
     proteinSelection.hideSelectedColumns(2, hiddenCols);
     MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
             proteinView, dnaView, dnaSelection, dnaHidden);
-    assertTrue(dnaHidden.getHiddenColumnsCopy().isEmpty());
+    assertEquals(0, dnaHidden.getNumberOfRegions());
 
     /*
      * Column 3 in protein picks up Seq1/P, Seq2/Q, Seq3/S which map to columns
@@ -959,9 +960,9 @@ public class MappingUtilsTest
     MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
             proteinView, dnaView, dnaSelection, dnaHidden);
     assertEquals("[0, 1, 2, 3]", dnaSelection.getSelected().toString());
-    hidden = dnaHidden.getHiddenColumnsCopy();
-    assertEquals(1, hidden.size());
-    assertEquals("[5, 10]", Arrays.toString(hidden.get(0)));
+    regions = dnaHidden.iterator();
+    assertEquals(1, dnaHidden.getNumberOfRegions());
+    assertEquals("[5, 10]", Arrays.toString(regions.next()));
 
     /*
      * Combine hiding columns 1 and 3 to get discontiguous hidden columns
@@ -974,10 +975,10 @@ public class MappingUtilsTest
     proteinSelection.hideSelectedColumns(3, hiddenCols);
     MappingUtils.mapColumnSelection(proteinSelection, hiddenCols,
             proteinView, dnaView, dnaSelection, dnaHidden);
-    hidden = dnaHidden.getHiddenColumnsCopy();
-    assertEquals(2, hidden.size());
-    assertEquals("[0, 3]", Arrays.toString(hidden.get(0)));
-    assertEquals("[5, 10]", Arrays.toString(hidden.get(1)));
+    regions = dnaHidden.iterator();
+    assertEquals(2, dnaHidden.getNumberOfRegions());
+    assertEquals("[0, 3]", Arrays.toString(regions.next()));
+    assertEquals("[5, 10]", Arrays.toString(regions.next()));
   }
 
   @Test(groups = { "Functional" })
@@ -1283,4 +1284,58 @@ public class MappingUtilsTest
     assertEquals(1, ranges.size());
     assertEquals(9, ranges.get(0)[1]);
   }
+
+  @Test(groups = "Functional")
+  public void testAddRange()
+  {
+    int[] range = { 1, 5 };
+    List<int[]> ranges = new ArrayList<>();
+  
+    // add to empty list:
+    MappingUtils.addRange(range, ranges);
+    assertEquals(1, ranges.size());
+    assertSame(range, ranges.get(0));
+  
+    // extend contiguous (same position):
+    MappingUtils.addRange(new int[] { 5, 10 }, ranges);
+    assertEquals(1, ranges.size());
+    assertEquals(1, ranges.get(0)[0]);
+    assertEquals(10, ranges.get(0)[1]);
+  
+    // extend contiguous (next position):
+    MappingUtils.addRange(new int[] { 11, 15 }, ranges);
+    assertEquals(1, ranges.size());
+    assertEquals(1, ranges.get(0)[0]);
+    assertEquals(15, ranges.get(0)[1]);
+  
+    // change direction: range is not merged:
+    MappingUtils.addRange(new int[] { 16, 10 }, ranges);
+    assertEquals(2, ranges.size());
+    assertEquals(16, ranges.get(1)[0]);
+    assertEquals(10, ranges.get(1)[1]);
+  
+    // extend reverse contiguous (same position):
+    MappingUtils.addRange(new int[] { 10, 8 }, ranges);
+    assertEquals(2, ranges.size());
+    assertEquals(16, ranges.get(1)[0]);
+    assertEquals(8, ranges.get(1)[1]);
+  
+    // extend reverse contiguous (next position):
+    MappingUtils.addRange(new int[] { 7, 6 }, ranges);
+    assertEquals(2, ranges.size());
+    assertEquals(16, ranges.get(1)[0]);
+    assertEquals(6, ranges.get(1)[1]);
+  
+    // change direction: range is not merged:
+    MappingUtils.addRange(new int[] { 6, 9 }, ranges);
+    assertEquals(3, ranges.size());
+    assertEquals(6, ranges.get(2)[0]);
+    assertEquals(9, ranges.get(2)[1]);
+  
+    // not contiguous: not merged
+    MappingUtils.addRange(new int[] { 11, 12 }, ranges);
+    assertEquals(4, ranges.size());
+    assertEquals(11, ranges.get(3)[0]);
+    assertEquals(12, ranges.get(3)[1]);
+  }
 }
diff --git a/test/jalview/util/Raw.csv b/test/jalview/util/Raw.csv
new file mode 100644
index 0000000..83d3452
--- /dev/null
+++ b/test/jalview/util/Raw.csv
@@ -0,0 +1,4 @@
+Seq1, Seq2, Seq3
+1.43, 2.34, 5.6,
+EMPTY, 1.2, 0.05,
+EMPTY, 5.4, 6.8,
\ No newline at end of file
diff --git a/test/jalview/util/test_Fams_for_probability_analysis b/test/jalview/util/test_Fams_for_probability_analysis
new file mode 100644
index 0000000..74fbab0
--- /dev/null
+++ b/test/jalview/util/test_Fams_for_probability_analysis
@@ -0,0 +1,13 @@
+# STOCKHOLM 1.0
+seq1 AW
+seq2 GW
+seq3 AW
+//
+# STOCKHOLM 1.0
+seq1 ATW
+seq2 ATI
+//
+# STOCKHOLM 1.0
+seq1 R-WW
+seq2 RAWW
+//
\ No newline at end of file
diff --git a/test/jalview/util/test_hmms_for_probability_analysis b/test/jalview/util/test_hmms_for_probability_analysis
new file mode 100644
index 0000000..b70d42b
--- /dev/null
+++ b/test/jalview/util/test_hmms_for_probability_analysis
@@ -0,0 +1,99 @@
+HMMER3/f [3.1b2 | February 2015]
+NAME  test1
+LENG  4
+ALPH  amino
+RF    no
+MM    no
+CONS  yes
+CS    no
+MAP   yes
+DATE  Fri Jul 21 06:35:06 2017
+NSEQ  3
+EFFN  3.000000
+CKSUM 657102310
+STATS LOCAL MSV       -5.0223  0.82341
+STATS LOCAL VITERBI   -4.9569  0.82341
+STATS LOCAL FORWARD   -2.0282  0.82341
+HMM          A        C        D        E        F        G        H        I        K        L        M        N        P        Q        R        S        T        V        W        Y   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.94296  5.20658  4.78882  4.52987  4.66525  2.54188  5.19553  2.25221  4.08549  3.87133  5.00250  4.55734  4.73106  4.65220  2.77287  3.67799  1.53923  3.75384  1.48526  4.84023
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.01083  4.92694  5.64929  0.61958  0.77255  0.00000        *
+      1   0.67027  4.79120  4.60974  4.51892  5.43734  1.28080  5.43621  4.90028  4.64310  4.61059  5.39837  4.28688  4.41468  4.80804  4.79047  3.08135  3.44468  4.10506  6.74908  5.67939      1 A - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.01083  4.92694  5.64929  0.61958  0.77255  0.48576  0.95510
+      2   5.43405  6.34487  5.85697  5.84679  4.39288  5.10370  5.65594  5.70664  5.69821  4.87848  6.25251  5.89664  5.70261  6.00722  5.60902  5.64576  5.80049  5.59366  0.08910  4.36301      2 W - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.01083  4.92694  5.64929  0.61958  0.77255  0.48576  0.95510
+      3   3.42384  5.23617  4.84601  4.77568  5.39247  4.01365  5.64153  4.72950  4.75585  4.52264  5.55782  4.69647  4.81267  5.08969  4.87301  3.64217  0.20934  4.25217  6.65833  5.63018      3 T - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.01083  4.92694  5.64929  0.61958  0.77255  0.48576  0.95510
+      4   3.53954  5.09963  4.71395  4.06038  4.20429  4.44020  4.65482  0.90152  3.16536  2.96072  4.13056  4.31689  4.83725  3.95143  1.46549  3.86829  3.78084  2.85654  5.74911  4.54685      4 i - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00730  4.92341        *  0.61958  0.77255  0.00000        *
+//
+HMMER3/f [3.1b2 | February 2015]
+NAME  test2
+LENG  3
+ALPH  amino
+RF    no
+MM    no
+CONS  yes
+CS    no
+MAP   yes
+DATE  Fri Jul 21 06:36:50 2017
+NSEQ  2
+EFFN  2.000000
+CKSUM 777554360
+STATS LOCAL MSV       -5.2452  0.95763
+STATS LOCAL VITERBI   -5.2886  0.95763
+STATS LOCAL FORWARD   -1.5134  0.95763
+HMM          A        C        D        E        F        G        H        I        K        L        M        N        P        Q        R        S        T        V        W        Y   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.33364  4.79082  4.44132  4.24796  3.91456  3.75718  4.85762  2.23342  4.16821  3.09137  4.29744  4.25088  4.41741  4.46803  4.31080  3.33397  1.39376  3.21010  2.54819  4.14914
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.01467  4.62483  5.34718  0.61958  0.77255  0.00000        *
+      1   0.32372  4.76536  4.42980  4.32857  5.00499  3.55951  5.22620  4.27004  4.37081  4.10495  5.08789  4.22499  4.36948  4.63911  4.51684  3.12947  3.46009  3.76842  6.33337  5.25783      1 A - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.01467  4.62483  5.34718  0.61958  0.77255  0.48576  0.95510
+      2   3.04414  4.87155  4.35068  4.21532  4.89213  3.66881  5.13994  4.14202  4.17893  3.96810  5.00600  4.23490  4.44590  4.53729  4.35178  3.25814  0.35496  3.73038  6.23308  5.12388      2 T - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.01467  4.62483  5.34718  0.61958  0.77255  0.48576  0.95510
+      3   3.41901  4.77187  4.98694  4.49106  3.10447  4.49364  4.52024  1.21391  4.22709  2.30875  3.57865  4.53952  4.83367  4.43564  4.31127  3.88439  3.66452  2.61326  1.44329  3.34125      3 i - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00990  4.62006        *  0.61958  0.77255  0.00000        *
+//
+HMMER3/f [3.1b2 | February 2015]
+NAME  test3
+LENG  4
+ALPH  amino
+RF    no
+MM    no
+CONS  yes
+CS    no
+MAP   yes
+DATE  Fri Jul 21 06:37:01 2017
+NSEQ  2
+EFFN  2.000000
+CKSUM 986955970
+STATS LOCAL MSV       -5.4578  0.80004
+STATS LOCAL VITERBI   -5.2499  0.80004
+STATS LOCAL FORWARD   -2.1856  0.80004
+HMM          A        C        D        E        F        G        H        I        K        L        M        N        P        Q        R        S        T        V        W        Y   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   2.16700  5.33023  4.57707  4.32329  4.15728  4.03215  4.83242  4.49728  3.73978  4.00181  5.18156  4.45520  4.63709  4.41734  1.53081  3.84281  4.10073  4.20172  0.82417  4.15750
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.01467  4.62483  5.34718  0.61958  0.77255  0.00000        *
+      1   4.09153  5.75008  4.67229  4.09411  5.31638  4.34678  4.67762  4.97541  2.93879  4.35023  5.37643  4.37234  4.85576  3.90366  0.27042  4.17197  4.33362  4.67489  6.11461  5.14175      1 R - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.39762  4.62483  1.14482  0.61958  0.77255  0.48576  0.95510
+      2   0.58385  4.42717  3.89187  3.72118  4.47383  3.23815  4.69159  3.65968  3.74862  3.52210  4.52478  3.76053  4.01438  4.05655  3.96007  2.78076  3.08518  3.24526  5.86063  4.71068      2 A - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.02145  4.24866  4.97100  0.61958  0.77255  0.27360  1.42978
+      3   4.82318  5.87391  5.36844  5.28961  3.81117  4.70308  5.10523  4.98084  5.06729  4.21822  5.56037  5.33222  5.28501  5.40387  5.04111  5.02415  5.17266  4.88017  0.16601  3.78547      3 W - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.01467  4.62483  5.34718  0.61958  0.77255  0.48576  0.95510
+      4   4.82318  5.87391  5.36844  5.28961  3.81117  4.70308  5.10523  4.98084  5.06729  4.21822  5.56037  5.33222  5.28501  5.40387  5.04111  5.02415  5.17266  4.88017  0.16601  3.78547      4 W - - -
+          2.68618  4.42225  2.77519  2.73123  3.46354  2.40513  3.72494  3.29354  2.67741  2.69355  4.24690  2.90347  2.73739  3.18146  2.89801  2.37887  2.77519  2.98518  4.58477  3.61503
+          0.00990  4.62006        *  0.61958  0.77255  0.00000        *
+//
\ No newline at end of file
diff --git a/test/jalview/ws/PDBSequenceFetcherTest.java b/test/jalview/ws/PDBSequenceFetcherTest.java
index 95863e7..cc3dca8 100644
--- a/test/jalview/ws/PDBSequenceFetcherTest.java
+++ b/test/jalview/ws/PDBSequenceFetcherTest.java
@@ -20,18 +20,22 @@
  */
 package jalview.ws;
 
+import static org.testng.Assert.assertEquals;
 import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.gui.JvOptionPane;
 import jalview.structure.StructureImportSettings;
 import jalview.structure.StructureImportSettings.StructureParser;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
+import java.util.Arrays;
 import java.util.List;
 
+import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
@@ -106,23 +110,76 @@ public class PDBSequenceFetcherTest
     testRetrieveProteinSeqFromPDB();
   }
 
+  private class TestRetrieveObject
+  {
+    String id;
+
+    int expectedHeight;
+
+    public TestRetrieveObject(String id, int expectedHeight)
+    {
+      super();
+      this.id = id;
+      this.expectedHeight = expectedHeight;
+    }
+
+  }
+
+  private List<TestRetrieveObject> toRetrieve = Arrays.asList(
+          new TestRetrieveObject("1QIP", 4),
+          new TestRetrieveObject("4IM2", 1));
+
   private void testRetrieveProteinSeqFromPDB() throws Exception
   {
     List<DbSourceProxy> sps = sf.getSourceProxy("PDB");
-    AlignmentI response = sps.get(0).getSequenceRecords("1QIP");
-    assertTrue(response != null);
-    assertTrue(response.getHeight() == 4);
-    for (SequenceI sq : response.getSequences())
+    StringBuilder errors = new StringBuilder();
+    for (TestRetrieveObject str : toRetrieve)
     {
-      assertTrue("No annotation transfered to sequence.",
-              sq.getAnnotation().length > 0);
-      assertTrue("No PDBEntry on sequence.",
-              sq.getAllPDBEntries().size() > 0);
-      org.testng.Assert
-              .assertEquals(sq.getEnd() - sq.getStart() + 1,
-                      sq.getLength(),
-                      "Sequence start/end doesn't match number of residues in sequence");
+      AlignmentI response = sps.get(0).getSequenceRecords(str.id);
+      assertTrue("No aligment for " + str.id, response != null);
+      assertEquals(response.getHeight(), str.expectedHeight,
+              "Number of chains for " + str.id);
+      for (SequenceI sq : response.getSequences())
+      {
+        assertTrue("No annotation transfered to sequence " + sq.getName(),
+                sq.getAnnotation().length > 0);
+        assertTrue("No PDBEntry on sequence " + sq.getName(),
+                sq.getAllPDBEntries().size() > 0);
+        // FIXME: should test that all residues extracted as sequences from
+        // chains in structure have a mapping to data in the structure
+        List<SequenceFeature> prev = null;
+        int lastp = -1;
+        for (int col = 1; col <= sq.getLength(); col++)
+        {
+          List<SequenceFeature> sf = sq.findFeatures(col, col, "RESNUM");
+          if (sf.size() != 1)
+          {
+            errors.append(
+                    str.id + ": " +
+                            "Expected one feature at column (position): "
+                            + (col - 1)
+                            + " (" + sq.findPosition(col - 1) + ")"
+                            + ": saw "
+                            + sf.size());
+            errors.append("\n");
+            if (prev != null)
+            {
+              errors.append("Last Feature was at position " + lastp + ": "
+                      + prev.get(0).toString());
+              errors.append("\n");
+            }
+          }
+          else
+          {
+            prev = sf;
+            lastp = sq.findPosition(col - 1);
+          }
+        }
+      }
+    }
+    if (errors.length() > 0)
+    {
+      Assert.fail(errors.toString());
     }
   }
-
 }
diff --git a/test/jalview/ws/dbsources/PfamFullTest.java b/test/jalview/ws/dbsources/PfamFullTest.java
new file mode 100644
index 0000000..b914a45
--- /dev/null
+++ b/test/jalview/ws/dbsources/PfamFullTest.java
@@ -0,0 +1,32 @@
+package jalview.ws.dbsources;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.bin.Cache;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+public class PfamFullTest
+{
+  @BeforeClass(alwaysRun = true)
+  public void setUp()
+  {
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
+  }
+
+  @Test(groups = "Functional")
+  public void testGetURL()
+  {
+    String path = "pfam.xfam.org/family/ABC/alignment/full";
+
+    // with default value for domain
+    String url = new PfamFull().getURL(" abc ");
+    assertEquals(url, "https://" + path);
+
+    // with override in properties
+    Cache.setProperty(Pfam.PFAM_BASEURL_KEY, "http://pfam.xfam.org");
+    url = new PfamFull().getURL(" abc ");
+    assertEquals(url, "http://" + path);
+  }
+}
diff --git a/test/jalview/ws/dbsources/PfamSeedTest.java b/test/jalview/ws/dbsources/PfamSeedTest.java
new file mode 100644
index 0000000..2fa1871
--- /dev/null
+++ b/test/jalview/ws/dbsources/PfamSeedTest.java
@@ -0,0 +1,32 @@
+package jalview.ws.dbsources;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.bin.Cache;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+public class PfamSeedTest
+{
+  @BeforeClass(alwaysRun = true)
+  public void setUp()
+  {
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
+  }
+
+  @Test(groups = "Functional")
+  public void testGetURL()
+  {
+    String path = "pfam.xfam.org/family/ABC/alignment/seed";
+
+    // with default value for domain
+    String url = new PfamSeed().getURL(" abc ");
+    assertEquals(url, "https://" + path);
+
+    // with override in properties
+    Cache.setProperty(Pfam.PFAM_BASEURL_KEY, "http://pfam.xfam.org");
+    url = new PfamSeed().getURL(" abc ");
+    assertEquals(url, "http://" + path);
+  }
+}
diff --git a/test/jalview/ws/dbsources/RfamFullTest.java b/test/jalview/ws/dbsources/RfamFullTest.java
new file mode 100644
index 0000000..cb60b14
--- /dev/null
+++ b/test/jalview/ws/dbsources/RfamFullTest.java
@@ -0,0 +1,32 @@
+package jalview.ws.dbsources;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.bin.Cache;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+public class RfamFullTest
+{
+  @BeforeClass(alwaysRun = true)
+  public void setUp()
+  {
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
+  }
+
+  @Test(groups = "Functional")
+  public void testGetURL()
+  {
+    String path = "rfam.xfam.org/family/ABC/alignment/full";
+
+    // with default value for domain
+    String url = new RfamFull().getURL(" abc ");
+    assertEquals(url, "https://" + path);
+
+    // with override in properties
+    Cache.setProperty(Rfam.RFAM_BASEURL_KEY, "http://rfam.xfam.org");
+    url = new RfamFull().getURL(" abc ");
+    assertEquals(url, "http://" + path);
+  }
+}
diff --git a/test/jalview/ws/dbsources/RfamSeedTest.java b/test/jalview/ws/dbsources/RfamSeedTest.java
new file mode 100644
index 0000000..5ca72c2
--- /dev/null
+++ b/test/jalview/ws/dbsources/RfamSeedTest.java
@@ -0,0 +1,32 @@
+package jalview.ws.dbsources;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.bin.Cache;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+public class RfamSeedTest
+{
+  @BeforeClass(alwaysRun = true)
+  public void setUp()
+  {
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
+  }
+
+  @Test(groups = "Functional")
+  public void testGetURL()
+  {
+    String path = "rfam.xfam.org/family/ABC/alignment/stockholm";
+
+    // with default value for domain
+    String url = new RfamSeed().getURL(" abc ");
+    assertEquals(url, "https://" + path);
+
+    // with override in properties
+    Cache.setProperty(Rfam.RFAM_BASEURL_KEY, "http://rfam.xfam.org");
+    url = new RfamSeed().getURL(" abc ");
+    assertEquals(url, "http://" + path);
+  }
+}
diff --git a/test/jalview/ws/dbsources/XfamFetcherTest.java b/test/jalview/ws/dbsources/XfamFetcherTest.java
index 573022d..51cff6e 100644
--- a/test/jalview/ws/dbsources/XfamFetcherTest.java
+++ b/test/jalview/ws/dbsources/XfamFetcherTest.java
@@ -58,7 +58,7 @@ public class XfamFetcherTest
   @Test(groups = { "External" })
   public void testPfamFullAndSeed() throws Exception
   {
-    PfamFull pff = new PfamFull();
+    Pfam pff = new PfamFull();
     PfamSeed pfseed = new PfamSeed();
 
     AlignmentI fullpf = pff.getSequenceRecords(pff.getTestQuery());
diff --git a/test/jalview/ws/sifts/SiftsClientTest.java b/test/jalview/ws/sifts/SiftsClientTest.java
index b92766e..75c1413 100644
--- a/test/jalview/ws/sifts/SiftsClientTest.java
+++ b/test/jalview/ws/sifts/SiftsClientTest.java
@@ -83,103 +83,103 @@ public class SiftsClientTest
   @BeforeTest(alwaysRun = true)
   public void populateExpectedMapping() throws SiftsException
   {
-    expectedMapping.put(51, new int[] { 1, 2 });
-    expectedMapping.put(52, new int[] { 2, 7 });
-    expectedMapping.put(53, new int[] { 3, 12 });
-    expectedMapping.put(54, new int[] { 4, 24 });
-    expectedMapping.put(55, new int[] { 5, 33 });
-    expectedMapping.put(56, new int[] { 6, 40 });
-    expectedMapping.put(57, new int[] { 7, 47 });
-    expectedMapping.put(58, new int[] { 8, 55 });
-    expectedMapping.put(59, new int[] { 9, 62 });
-    expectedMapping.put(60, new int[] { 10, 69 });
-    expectedMapping.put(61, new int[] { 11, 76 });
-    expectedMapping.put(62, new int[] { 12, 83 });
-    expectedMapping.put(63, new int[] { 13, 87 });
-    expectedMapping.put(64, new int[] { 14, 95 });
-    expectedMapping.put(65, new int[] { 15, 102 });
-    expectedMapping.put(66, new int[] { 16, 111 });
-    expectedMapping.put(67, new int[] { 17, 122 });
-    expectedMapping.put(68, new int[] { 18, 131 });
-    expectedMapping.put(69, new int[] { 19, 137 });
-    expectedMapping.put(70, new int[] { 20, 144 });
-    expectedMapping.put(71, new int[] { 21, 152 });
-    expectedMapping.put(72, new int[] { 22, 160 });
-    expectedMapping.put(73, new int[] { 23, 167 });
-    expectedMapping.put(74, new int[] { 24, 179 });
-    expectedMapping.put(75, new int[] { 25, 187 });
-    expectedMapping.put(76, new int[] { 26, 195 });
-    expectedMapping.put(77, new int[] { 27, 203 });
-    expectedMapping.put(78, new int[] { 28, 208 });
-    expectedMapping.put(79, new int[] { 29, 213 });
-    expectedMapping.put(80, new int[] { 30, 222 });
-    expectedMapping.put(81, new int[] { 31, 231 });
-    expectedMapping.put(82, new int[] { 32, 240 });
-    expectedMapping.put(83, new int[] { 33, 244 });
-    expectedMapping.put(84, new int[] { 34, 252 });
-    expectedMapping.put(85, new int[] { 35, 260 });
-    expectedMapping.put(86, new int[] { 36, 268 });
-    expectedMapping.put(87, new int[] { 37, 275 });
-    expectedMapping.put(88, new int[] { 38, 287 });
-    expectedMapping.put(89, new int[] { 39, 293 });
-    expectedMapping.put(90, new int[] { 40, 299 });
-    expectedMapping.put(91, new int[] { 41, 310 });
-    expectedMapping.put(92, new int[] { 42, 315 });
-    expectedMapping.put(93, new int[] { 43, 319 });
-    expectedMapping.put(94, new int[] { 44, 325 });
-    expectedMapping.put(95, new int[] { 45, 331 });
-    expectedMapping.put(96, new int[] { 46, 337 });
-    expectedMapping.put(97, new int[] { 47, 343 });
-    expectedMapping.put(98, new int[] { 48, 349 });
-    expectedMapping.put(99, new int[] { 49, 354 });
-    expectedMapping.put(100, new int[] { 50, 358 });
-    expectedMapping.put(101, new int[] { 51, 367 });
-    expectedMapping.put(102, new int[] { 52, 375 });
-    expectedMapping.put(103, new int[] { 53, 384 });
-    expectedMapping.put(104, new int[] { 54, 391 });
-    expectedMapping.put(105, new int[] { 55, 395 });
-    expectedMapping.put(106, new int[] { 56, 401 });
-    expectedMapping.put(107, new int[] { 57, 409 });
-    expectedMapping.put(108, new int[] { 58, 417 });
-    expectedMapping.put(109, new int[] { 59, 426 });
-    expectedMapping.put(110, new int[] { 60, 434 });
-    expectedMapping.put(111, new int[] { 61, 442 });
-    expectedMapping.put(112, new int[] { 62, 451 });
-    expectedMapping.put(113, new int[] { 63, 457 });
-    expectedMapping.put(114, new int[] { 64, 468 });
-    expectedMapping.put(115, new int[] { 65, 476 });
-    expectedMapping.put(116, new int[] { 66, 484 });
-    expectedMapping.put(117, new int[] { 67, 492 });
-    expectedMapping.put(118, new int[] { 68, 500 });
-    expectedMapping.put(119, new int[] { 69, 509 });
-    expectedMapping.put(120, new int[] { 70, 517 });
-    expectedMapping.put(121, new int[] { 71, 525 });
-    expectedMapping.put(122, new int[] { 72, 534 });
-    expectedMapping.put(123, new int[] { 73, 538 });
-    expectedMapping.put(124, new int[] { 74, 552 });
-    expectedMapping.put(125, new int[] { 75, 559 });
-    expectedMapping.put(126, new int[] { 76, 567 });
-    expectedMapping.put(127, new int[] { 77, 574 });
-    expectedMapping.put(128, new int[] { 78, 580 });
-    expectedMapping.put(129, new int[] { 79, 585 });
-    expectedMapping.put(130, new int[] { 80, 590 });
-    expectedMapping.put(131, new int[] { 81, 602 });
-    expectedMapping.put(132, new int[] { 82, 609 });
-    expectedMapping.put(133, new int[] { 83, 616 });
-    expectedMapping.put(134, new int[] { 84, 622 });
-    expectedMapping.put(135, new int[] { 85, 630 });
-    expectedMapping.put(136, new int[] { 86, 637 });
-    expectedMapping.put(137, new int[] { 87, 644 });
-    expectedMapping.put(138, new int[] { 88, 652 });
-    expectedMapping.put(139, new int[] { 89, 661 });
-    expectedMapping.put(140, new int[] { 90, 668 });
-    expectedMapping.put(141, new int[] { 91, 678 });
-    expectedMapping.put(142, new int[] { 92, 687 });
-    expectedMapping.put(143, new int[] { 93, 696 });
-    expectedMapping.put(144, new int[] { 94, 705 });
-    expectedMapping.put(145, new int[] { 95, 714 });
-    expectedMapping.put(146, new int[] { 96, 722 });
-    expectedMapping.put(147, new int[] { 97, 729 });
+    expectedMapping.put(51, new int[] { 1, 2, 1 });
+    expectedMapping.put(52, new int[] { 2, 7, 2 });
+    expectedMapping.put(53, new int[] { 3, 12, 3 });
+    expectedMapping.put(54, new int[] { 4, 24, 4 });
+    expectedMapping.put(55, new int[] { 5, 33, 5 });
+    expectedMapping.put(56, new int[] { 6, 40, 6 });
+    expectedMapping.put(57, new int[] { 7, 47, 7 });
+    expectedMapping.put(58, new int[] { 8, 55, 8 });
+    expectedMapping.put(59, new int[] { 9, 62, 9 });
+    expectedMapping.put(60, new int[] { 10, 69, 10 });
+    expectedMapping.put(61, new int[] { 11, 76, 11 });
+    expectedMapping.put(62, new int[] { 12, 83, 12 });
+    expectedMapping.put(63, new int[] { 13, 87, 13 });
+    expectedMapping.put(64, new int[] { 14, 95, 14 });
+    expectedMapping.put(65, new int[] { 15, 102, 15 });
+    expectedMapping.put(66, new int[] { 16, 111, 16 });
+    expectedMapping.put(67, new int[] { 17, 122, 17 });
+    expectedMapping.put(68, new int[] { 18, 131, 18 });
+    expectedMapping.put(69, new int[] { 19, 137, 19 });
+    expectedMapping.put(70, new int[] { 20, 144, 20 });
+    expectedMapping.put(71, new int[] { 21, 152, 21 });
+    expectedMapping.put(72, new int[] { 22, 160, 22 });
+    expectedMapping.put(73, new int[] { 23, 167, 23 });
+    expectedMapping.put(74, new int[] { 24, 179, 24 });
+    expectedMapping.put(75, new int[] { 25, 187, 25 });
+    expectedMapping.put(76, new int[] { 26, 195, 26 });
+    expectedMapping.put(77, new int[] { 27, 203, 27 });
+    expectedMapping.put(78, new int[] { 28, 208, 28 });
+    expectedMapping.put(79, new int[] { 29, 213, 29 });
+    expectedMapping.put(80, new int[] { 30, 222, 30 });
+    expectedMapping.put(81, new int[] { 31, 231, 31 });
+    expectedMapping.put(82, new int[] { 32, 240, 32 });
+    expectedMapping.put(83, new int[] { 33, 244, 33 });
+    expectedMapping.put(84, new int[] { 34, 252, 34 });
+    expectedMapping.put(85, new int[] { 35, 260, 35 });
+    expectedMapping.put(86, new int[] { 36, 268, 36 });
+    expectedMapping.put(87, new int[] { 37, 275, 37 });
+    expectedMapping.put(88, new int[] { 38, 287, 38 });
+    expectedMapping.put(89, new int[] { 39, 293, 39 });
+    expectedMapping.put(90, new int[] { 40, 299, 40 });
+    expectedMapping.put(91, new int[] { 41, 310, 41 });
+    expectedMapping.put(92, new int[] { 42, 315, 42 });
+    expectedMapping.put(93, new int[] { 43, 319, 43 });
+    expectedMapping.put(94, new int[] { 44, 325, 44 });
+    expectedMapping.put(95, new int[] { 45, 331, 45 });
+    expectedMapping.put(96, new int[] { 46, 337, 46 });
+    expectedMapping.put(97, new int[] { 47, 343, 47 });
+    expectedMapping.put(98, new int[] { 48, 349, 48 });
+    expectedMapping.put(99, new int[] { 49, 354, 49 });
+    expectedMapping.put(100, new int[] { 50, 358, 50 });
+    expectedMapping.put(101, new int[] { 51, 367, 51 });
+    expectedMapping.put(102, new int[] { 52, 375, 52 });
+    expectedMapping.put(103, new int[] { 53, 384, 53 });
+    expectedMapping.put(104, new int[] { 54, 391, 54 });
+    expectedMapping.put(105, new int[] { 55, 395, 55 });
+    expectedMapping.put(106, new int[] { 56, 401, 56 });
+    expectedMapping.put(107, new int[] { 57, 409, 57 });
+    expectedMapping.put(108, new int[] { 58, 417, 58 });
+    expectedMapping.put(109, new int[] { 59, 426, 59 });
+    expectedMapping.put(110, new int[] { 60, 434, 60 });
+    expectedMapping.put(111, new int[] { 61, 442, 61 });
+    expectedMapping.put(112, new int[] { 62, 451, 62 });
+    expectedMapping.put(113, new int[] { 63, 457, 63 });
+    expectedMapping.put(114, new int[] { 64, 468, 64 });
+    expectedMapping.put(115, new int[] { 65, 476, 65 });
+    expectedMapping.put(116, new int[] { 66, 484, 66 });
+    expectedMapping.put(117, new int[] { 67, 492, 67 });
+    expectedMapping.put(118, new int[] { 68, 500, 68 });
+    expectedMapping.put(119, new int[] { 69, 509, 69 });
+    expectedMapping.put(120, new int[] { 70, 517, 70 });
+    expectedMapping.put(121, new int[] { 71, 525, 71 });
+    expectedMapping.put(122, new int[] { 72, 534, 72 });
+    expectedMapping.put(123, new int[] { 73, 538, 73 });
+    expectedMapping.put(124, new int[] { 74, 552, 74 });
+    expectedMapping.put(125, new int[] { 75, 559, 75 });
+    expectedMapping.put(126, new int[] { 76, 567, 76 });
+    expectedMapping.put(127, new int[] { 77, 574, 77 });
+    expectedMapping.put(128, new int[] { 78, 580, 78 });
+    expectedMapping.put(129, new int[] { 79, 585, 79 });
+    expectedMapping.put(130, new int[] { 80, 590, 80 });
+    expectedMapping.put(131, new int[] { 81, 602, 81 });
+    expectedMapping.put(132, new int[] { 82, 609, 82 });
+    expectedMapping.put(133, new int[] { 83, 616, 83 });
+    expectedMapping.put(134, new int[] { 84, 622, 84 });
+    expectedMapping.put(135, new int[] { 85, 630, 85 });
+    expectedMapping.put(136, new int[] { 86, 637, 86 });
+    expectedMapping.put(137, new int[] { 87, 644, 87 });
+    expectedMapping.put(138, new int[] { 88, 652, 88 });
+    expectedMapping.put(139, new int[] { 89, 661, 89 });
+    expectedMapping.put(140, new int[] { 90, 668, 90 });
+    expectedMapping.put(141, new int[] { 91, 678, 91 });
+    expectedMapping.put(142, new int[] { 92, 687, 92 });
+    expectedMapping.put(143, new int[] { 93, 696, 93 });
+    expectedMapping.put(144, new int[] { 94, 705, 94 });
+    expectedMapping.put(145, new int[] { 95, 714, 95 });
+    expectedMapping.put(146, new int[] { 96, 722, 96 });
+    expectedMapping.put(147, new int[] { 97, 729, 97 });
   }
 
   @BeforeTest(alwaysRun = true)
@@ -311,7 +311,7 @@ public class SiftsClientTest
     atom.atomIndex = 7;
     atoms.add(atom);
     int actualAtomIndex = siftsClient.getAtomIndex(1, atoms);
-    Assert.assertEquals(actualAtomIndex, -1);
+    Assert.assertEquals(actualAtomIndex, siftsClient.UNASSIGNED);
     actualAtomIndex = siftsClient.getAtomIndex(43, atoms);
     Assert.assertEquals(actualAtomIndex, 7);
   }