formatting

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index ee67b55..8872be0 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -510,7 +510,8 @@ public class Jalview2XML
 
         if (av.isHiddenRepSequence(jal.getSequenceAt(i)))
         {
-          jalview.datamodel.SequenceI[] reps = av.getRepresentedSequences(jal.getSequenceAt(i)).getSequencesInOrder(jal);
+          jalview.datamodel.SequenceI[] reps = av.getRepresentedSequences(
+                  jal.getSequenceAt(i)).getSequencesInOrder(jal);
 
           for (int h = 0; h < reps.length; h++)
           {
@@ -617,8 +618,8 @@ public class Jalview2XML
 
                 for (int smap = 0; smap < jmol.jmb.sequence[peid].length; smap++)
                 {
-//                  if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1)
-                  if (jds==jmol.jmb.sequence[peid][smap])
+                  // if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1)
+                  if (jds == jmol.jmb.sequence[peid][smap])
                   {
                     StructureState state = new StructureState();
                     state.setVisible(true);
@@ -870,8 +871,10 @@ public class Jalview2XML
 
         an.setLabel(aa[i].label);
 
-        if (aa[i] == av.getAlignmentQualityAnnot() || aa[i] == av.getAlignmentConservationAnnotation()
-                || aa[i] == av.getAlignmentConsensusAnnotation() || aa[i].autoCalculated)
+        if (aa[i] == av.getAlignmentQualityAnnot()
+                || aa[i] == av.getAlignmentConservationAnnotation()
+                || aa[i] == av.getAlignmentConsensusAnnotation()
+                || aa[i].autoCalculated)
         {
           // new way of indicating autocalculated annotation -
           an.setAutoCalculated(aa[i].autoCalculated);
@@ -881,7 +884,7 @@ public class Jalview2XML
           an.setScore(aa[i].getScore());
         }
 
-        if (aa[i].getCalcId()!=null)
+        if (aa[i].getCalcId() != null)
         {
           calcIdSet.add(aa[i].getCalcId());
           an.setCalcId(aa[i].getCalcId());
@@ -941,7 +944,7 @@ public class Jalview2XML
     {
       JGroup[] groups = new JGroup[jal.getGroups().size()];
       int i = -1;
-      for (jalview.datamodel.SequenceGroup sg:jal.getGroups())
+      for (jalview.datamodel.SequenceGroup sg : jal.getGroups())
       {
         groups[++i] = new JGroup();
 
@@ -1195,7 +1198,8 @@ public class Jalview2XML
         fs.addSetting(setting);
         settingsAdded.addElement(key);
       }
-      en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups.keySet().iterator();
+      en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups
+              .keySet().iterator();
       Vector groupsAdded = new Vector();
       while (en.hasNext())
       {
@@ -1292,7 +1296,7 @@ public class Jalview2XML
       vCalcIdParam.addServiceURL(settings.getServiceURI());
       // generic URI allowing a third party to resolve another instance of the
       // service used for this calculation
-      for (String urls:settings.getServiceURLs())
+      for (String urls : settings.getServiceURLs())
       {
         vCalcIdParam.addServiceURL(urls);
       }
@@ -1311,8 +1315,8 @@ public class Jalview2XML
       // need to be able to recover 1) settings 2) user-defined presets or
       // recreate settings from preset 3) predefined settings provided by
       // service - or settings that can be transferred (or discarded)
-      vCalcIdParam.setParameters(settings
-              .getWsParamFile().replace("\n", "|\\n|"));
+      vCalcIdParam.setParameters(settings.getWsParamFile().replace("\n",
+              "|\\n|"));
       vCalcIdParam.setAutoUpdate(settings.isAutoUpdate());
       // todo - decide if updateImmediately is needed for any projects.
 
@@ -1326,33 +1330,47 @@ public class Jalview2XML
   {
     if (calcIdParam.getVersion().equals("1.0"))
     {
-      Jws2Instance service=Jws2Discoverer.getDiscoverer().getPreferredServiceFor(calcIdParam.getServiceURL());
-      if (service!=null)
+      Jws2Instance service = Jws2Discoverer.getDiscoverer()
+              .getPreferredServiceFor(calcIdParam.getServiceURL());
+      if (service != null)
       {
-        WsParamSetI parmSet=null;
-        try {
-          parmSet = service.getParamStore().parseServiceParameterFile(calcIdParam.getName(), calcIdParam.getDescription(), calcIdParam.getServiceURL(), calcIdParam.getParameters().replace("|\\n|", "\n"));
+        WsParamSetI parmSet = null;
+        try
+        {
+          parmSet = service.getParamStore().parseServiceParameterFile(
+                  calcIdParam.getName(), calcIdParam.getDescription(),
+                  calcIdParam.getServiceURL(),
+                  calcIdParam.getParameters().replace("|\\n|", "\n"));
         } catch (IOException x)
         {
-          warn("Couldn't parse parameter data for "+calcIdParam.getCalcId(), x);
+          warn("Couldn't parse parameter data for "
+                  + calcIdParam.getCalcId(), x);
           return false;
         }
-        List<ArgumentI> argList=null;
-        if (calcIdParam.getName().length()>0) {
-          parmSet = service.getParamStore().getPreset(calcIdParam.getName());
-          if (parmSet!=null)
+        List<ArgumentI> argList = null;
+        if (calcIdParam.getName().length() > 0)
+        {
+          parmSet = service.getParamStore()
+                  .getPreset(calcIdParam.getName());
+          if (parmSet != null)
           {
-            // TODO : check we have a good match with settings in AACons - otherwise we'll need to create a new preset
+            // TODO : check we have a good match with settings in AACons -
+            // otherwise we'll need to create a new preset
           }
         }
-        else {
+        else
+        {
           argList = parmSet.getArguments();
-          parmSet=null;
+          parmSet = null;
         }
-        AAConsSettings settings = new AAConsSettings(calcIdParam.isAutoUpdate(), service, parmSet, argList);
-        av.setCalcIdSettingsFor(calcIdParam.getCalcId(), settings, calcIdParam.isNeedsUpdate());
+        AAConsSettings settings = new AAConsSettings(
+                calcIdParam.isAutoUpdate(), service, parmSet, argList);
+        av.setCalcIdSettingsFor(calcIdParam.getCalcId(), settings,
+                calcIdParam.isNeedsUpdate());
         return true;
-      } else {
+      }
+      else
+      {
         warn("Cannot resolve a service for the parameters used in this project. Try configuring a JABAWS server.");
         return false;
       }
@@ -1360,6 +1378,7 @@ public class Jalview2XML
     throw new Error("Unsupported Version for calcIdparam "
             + calcIdParam.toString());
   }
+
   /**
    * External mapping between jalview objects and objects yielding a valid and
    * unique object ID string. This is null for normal Jalview project IO, but
@@ -1371,7 +1390,7 @@ public class Jalview2XML
   /**
    * Construct a unique ID for jvobj using either existing bindings or if none
    * exist, the result of the hashcode call for the object.
-   *
+   * 
    * @param jvobj
    *          jalview data object
    * @return unique ID for referring to jvobj
@@ -1402,7 +1421,7 @@ public class Jalview2XML
 
   /**
    * return local jalview object mapped to ID, if it exists
-   *
+   * 
    * @param idcode
    *          (may be null)
    * @return null or object bound to idcode
@@ -1638,7 +1657,7 @@ public class Jalview2XML
 
   /**
    * Load a jalview project archive from a jar file
-   *
+   * 
    * @param file
    *          - HTTP URL or filename
    */
@@ -1708,7 +1727,7 @@ public class Jalview2XML
    * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence
    * themselves. Any null fields will be initialised with default values,
    * non-null fields are left alone.
-   *
+   * 
    * @param jprovider
    * @return
    */
@@ -1929,7 +1948,7 @@ public class Jalview2XML
         }
         ;
         out.close();
-        String t=outFile.getAbsolutePath();
+        String t = outFile.getAbsolutePath();
         alreadyLoadedPDB.put(pdbId, t);
         return t;
       }
@@ -1966,7 +1985,7 @@ public class Jalview2XML
 
   /**
    * Load alignment frame from jalview XML DOM object
-   *
+   * 
    * @param object
    *          DOM
    * @param file
@@ -2027,8 +2046,7 @@ public class Jalview2XML
           hiddenSeqs = new Vector();
         }
 
-        hiddenSeqs.addElement(seqRefIds
-                .get(seqId));
+        hiddenSeqs.addElement(seqRefIds.get(seqId));
       }
 
     }
@@ -2368,7 +2386,7 @@ public class Jalview2XML
         }
         if (an[i].hasBelowAlignment())
         {
-          jaa.belowAlignment=an[i].isBelowAlignment();
+          jaa.belowAlignment = an[i].isBelowAlignment();
         }
         jaa.setCalcId(an[i].getCalcId());
 
@@ -2735,13 +2753,12 @@ public class Jalview2XML
               }
               if (ids[p].getFile() != null)
               {
-                File mapkey=new File(ids[p].getFile());
+                File mapkey = new File(ids[p].getFile());
                 Object[] seqstrmaps = (Object[]) ((Hashtable) jmoldat[2])
                         .get(mapkey);
                 if (seqstrmaps == null)
                 {
-                  ((Hashtable) jmoldat[2]).put(
-                          mapkey,
+                  ((Hashtable) jmoldat[2]).put(mapkey,
                           seqstrmaps = new Object[]
                           { pdbFile, ids[p].getId(), new Vector(),
                               new Vector() });
@@ -2838,25 +2855,28 @@ public class Jalview2XML
               {
                 newFileLoc = new StringBuffer();
               }
-              do {
+              do
+              {
                 // look for next filename in load statement
-              newFileLoc.append(state.substring(cp,
-                      ncp = (state.indexOf("\"", ncp + 1) + 1)));
-              String oldfilenam = state.substring(ncp,
-                      ecp = state.indexOf("\"", ncp));
-              // recover the new mapping data for this old filename
-              // have to normalize filename - since Jmol and jalview do filename
-              // translation differently.
-              Object[] filedat = oldFiles.get(new File(oldfilenam));
-              newFileLoc.append(Platform.escapeString((String) filedat[0]));
-              pdbfilenames.addElement((String) filedat[0]);
-              pdbids.addElement((String) filedat[1]);
-              seqmaps.addElement(((Vector<SequenceI>) filedat[2])
-                      .toArray(new SequenceI[0]));
-              newFileLoc.append("\"");
-              cp = ecp + 1; // advance beyond last \" and set cursor so we can
-                            // look for next file statement.
-              } while ((ncp=state.indexOf("/*file*/",cp))>-1);
+                newFileLoc.append(state.substring(cp,
+                        ncp = (state.indexOf("\"", ncp + 1) + 1)));
+                String oldfilenam = state.substring(ncp,
+                        ecp = state.indexOf("\"", ncp));
+                // recover the new mapping data for this old filename
+                // have to normalize filename - since Jmol and jalview do
+                // filename
+                // translation differently.
+                Object[] filedat = oldFiles.get(new File(oldfilenam));
+                newFileLoc.append(Platform
+                        .escapeString((String) filedat[0]));
+                pdbfilenames.addElement((String) filedat[0]);
+                pdbids.addElement((String) filedat[1]);
+                seqmaps.addElement(((Vector<SequenceI>) filedat[2])
+                        .toArray(new SequenceI[0]));
+                newFileLoc.append("\"");
+                cp = ecp + 1; // advance beyond last \" and set cursor so we can
+                              // look for next file statement.
+              } while ((ncp = state.indexOf("/*file*/", cp)) > -1);
             }
             if (cp > 0)
             {
@@ -2992,8 +3012,7 @@ public class Jalview2XML
             }
             if (usetoColourbyseq)
             {
-              comp.useAlignmentPanelForColourbyseq(ap,
-                      !jmolColouring);
+              comp.useAlignmentPanelForColourbyseq(ap, !jmolColouring);
             }
             else
             {
@@ -3020,8 +3039,8 @@ public class Jalview2XML
 
     for (int i = 0; i < JSEQ.length; i++)
     {
-      af.viewport.setSequenceColour(af.viewport.getAlignment().getSequenceAt(i),
-              new java.awt.Color(JSEQ[i].getColour()));
+      af.viewport.setSequenceColour(af.viewport.getAlignment()
+              .getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour()));
     }
 
     af.viewport.gatherViewsHere = view.getGatheredViews();
@@ -3143,8 +3162,8 @@ public class Jalview2XML
               if (view.getAnnotationColours().getColourScheme()
                       .equals("None"))
               {
-                cs = new AnnotationColourGradient(
-                        af.viewport.getAlignment().getAlignmentAnnotation()[i],
+                cs = new AnnotationColourGradient(af.viewport
+                        .getAlignment().getAlignmentAnnotation()[i],
                         new java.awt.Color(view.getAnnotationColours()
                                 .getMinColour()), new java.awt.Color(view
                                 .getAnnotationColours().getMaxColour()),
@@ -3153,16 +3172,16 @@ public class Jalview2XML
               else if (view.getAnnotationColours().getColourScheme()
                       .startsWith("ucs"))
               {
-                cs = new AnnotationColourGradient(
-                        af.viewport.getAlignment().getAlignmentAnnotation()[i],
+                cs = new AnnotationColourGradient(af.viewport
+                        .getAlignment().getAlignmentAnnotation()[i],
                         GetUserColourScheme(jms, view
                                 .getAnnotationColours().getColourScheme()),
                         view.getAnnotationColours().getAboveThreshold());
               }
               else
               {
-                cs = new AnnotationColourGradient(
-                        af.viewport.getAlignment().getAlignmentAnnotation()[i],
+                cs = new AnnotationColourGradient(af.viewport
+                        .getAlignment().getAlignmentAnnotation()[i],
                         ColourSchemeProperty.getColour(al, view
                                 .getAnnotationColours().getColourScheme()),
                         view.getAnnotationColours().getAboveThreshold());
@@ -3173,8 +3192,8 @@ public class Jalview2XML
               {
                 for (int g = 0; g < al.getGroups().size(); g++)
                 {
-                  jalview.datamodel.SequenceGroup sg = al
-                          .getGroups().get(g);
+                  jalview.datamodel.SequenceGroup sg = al.getGroups()
+                          .get(g);
 
                   if (sg.cs == null)
                   {
@@ -3193,8 +3212,8 @@ public class Jalview2XML
                    * view.getAnnotationColours().getAboveThreshold()); } else
                    */
                   {
-                    sg.cs = new AnnotationColourGradient(
-                            af.viewport.getAlignment().getAlignmentAnnotation()[i],
+                    sg.cs = new AnnotationColourGradient(af.viewport
+                            .getAlignment().getAlignmentAnnotation()[i],
                             sg.cs, view.getAnnotationColours()
                                     .getAboveThreshold());
                   }
@@ -3242,8 +3261,8 @@ public class Jalview2XML
     }
     if (view.hasIgnoreGapsinConsensus())
     {
-      af.viewport.setIgnoreGapsConsensus(view
-              .getIgnoreGapsinConsensus(), null);
+      af.viewport.setIgnoreGapsConsensus(view.getIgnoreGapsinConsensus(),
+              null);
     }
     if (view.hasFollowHighlight())
     {
@@ -3415,14 +3434,16 @@ public class Jalview2XML
       }
       for (JvAnnotRow auan : autoAlan)
       {
-        visan.put(auan.template.label+(auan.template.getCalcId()==null ? "" : "\t"+auan.template.getCalcId()), auan);
+        visan.put(auan.template.label
+                + (auan.template.getCalcId() == null ? "" : "\t"
+                        + auan.template.getCalcId()), auan);
       }
       int hSize = al.getAlignmentAnnotation().length;
       ArrayList<JvAnnotRow> reorder = new ArrayList<JvAnnotRow>();
       // work through any autoCalculated annotation already on the view
       // removing it if it should be placed in a different location on the
       // annotation panel.
-      List<String> remains=new ArrayList(visan.keySet());
+      List<String> remains = new ArrayList(visan.keySet());
       for (int h = 0; h < hSize; h++)
       {
         jalview.datamodel.AlignmentAnnotation jalan = al
@@ -3430,12 +3451,12 @@ public class Jalview2XML
         if (jalan.autoCalculated)
         {
           String k;
-          JvAnnotRow valan = visan.get(k=jalan.label);
-          if (jalan.getCalcId()!=null)
+          JvAnnotRow valan = visan.get(k = jalan.label);
+          if (jalan.getCalcId() != null)
           {
-            valan = visan.get(k=jalan.label+ "\t"+jalan.getCalcId());
+            valan = visan.get(k = jalan.label + "\t" + jalan.getCalcId());
           }
-          
+
           if (valan != null)
           {
             // delete the auto calculated row from the alignment
@@ -3462,11 +3483,13 @@ public class Jalview2XML
           }
         }
       }
-      // Add any (possibly stale) autocalculated rows that were not appended to the view during construction
-      for (String other:remains)
+      // Add any (possibly stale) autocalculated rows that were not appended to
+      // the view during construction
+      for (String other : remains)
       {
-        JvAnnotRow othera=visan.get(other);
-        if (othera!=nullAnnot && othera.template.getCalcId()!=null && othera.template.getCalcId().length()>0)
+        JvAnnotRow othera = visan.get(other);
+        if (othera != nullAnnot && othera.template.getCalcId() != null
+                && othera.template.getCalcId().length() > 0)
         {
           reorder.add(othera);
         }

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index 8588bf2..e527c10 100644 (file)
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -560,7 +560,6 @@ public class AnnotationRenderer
               {
                 aa[gg].visible = false;
               }
-
               if (aa[gg].graphMax > groupmax)
               {
                 groupmax = aa[gg].graphMax;

diff --git a/src/jalview/ws/jws2/AAConsClient.java b/src/jalview/ws/jws2/AAConsClient.java
index 42a7bdb..c565915 100644 (file)
--- a/src/jalview/ws/jws2/AAConsClient.java
+++ b/src/jalview/ws/jws2/AAConsClient.java
@@ -28,19 +28,27 @@ public class AAConsClient extends JabawsAlignCalcWorker
     alignedSeqs = true;
     nucleotidesAllowed = false;
     proteinAllowed = true;
-    gapMap=new boolean[0];
+    gapMap = new boolean[0];
     initViewportParams();
   }
 
   protected void initViewportParams()
   {
-    ((jalview.gui.AlignViewport) alignViewport).setCalcIdSettingsFor(getCalcId(), new AAConsSettings(true, service, this.preset, (arguments!=null) ?  JabaParamStore.getJwsArgsfromJaba(arguments) : null), true);
+    ((jalview.gui.AlignViewport) alignViewport).setCalcIdSettingsFor(
+            getCalcId(),
+            new AAConsSettings(true, service, this.preset,
+                    (arguments != null) ? JabaParamStore
+                            .getJwsArgsfromJaba(arguments) : null), true);
   }
+
   @Override
-  public void updateParameters(WsParamSetI newpreset, java.util.List<Argument> newarguments) {
+  public void updateParameters(WsParamSetI newpreset,
+          java.util.List<Argument> newarguments)
+  {
     super.updateParameters(newpreset, newarguments);
     initViewportParams();
   };
+
   public String getServiceActionText()
   {
     return "calculating Amino acid consensus using AACons service";
@@ -97,13 +105,10 @@ public class AAConsClient extends JabawsAlignCalcWorker
 
   public static void removeAAConsAnnotation(AlignmentPanel alignPanel)
   {
-    for (AlignmentAnnotation aa: alignPanel.getAlignment().findAnnotation(SequenceAnnotationWSClient.AAConsCalcId))
+    for (AlignmentAnnotation aa : alignPanel.getAlignment().findAnnotation(
+            SequenceAnnotationWSClient.AAConsCalcId))
     {
       alignPanel.getAlignment().deleteAnnotation(aa);
     }
-    // List<AlignmentAnnotation>
-    // ourannots=alignPanel.getAlignment().findAnnotation(Screen3D.)
-    // TODO Auto-generated method stub
-
   }
 }

diff --git a/src/jalview/ws/jws2/JabawsAlignCalcWorker.java b/src/jalview/ws/jws2/JabawsAlignCalcWorker.java
index d8807e7..58cb3ac 100644 (file)
--- a/src/jalview/ws/jws2/JabawsAlignCalcWorker.java
+++ b/src/jalview/ws/jws2/JabawsAlignCalcWorker.java
@@ -41,6 +41,7 @@ import compbio.metadata.WrongParameterException;
 public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
 {
   Jws2Instance service;
+
   @SuppressWarnings("unchecked")
   protected SequenceAnnotation aaservice;
 
@@ -84,7 +85,7 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
    * reconfigure and restart the AAConsClient. This method will spawn a new
    * thread that will wait until any current jobs are finished, modify the
    * parameters and restart the conservation calculation with the new values.
-   *
+   * 
    * @param newpreset
    * @param newarguments
    */
@@ -128,7 +129,7 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
     int serverErrorsLeft = 3;
 
     String rslt = "JOB NOT DEFINED";
-    StringBuffer msg=new StringBuffer();
+    StringBuffer msg = new StringBuffer();
     try
     {
       if (checkDone())
@@ -151,7 +152,7 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
         guiProgress.setProgressBar("JABA " + getServiceActionText(),
                 progressId = System.currentTimeMillis());
       }
-      if (preset == null && arguments==null)
+      if (preset == null && arguments == null)
       {
         rslt = aaservice.analize(seqs);
       }
@@ -310,19 +311,22 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
       if (ap != null)
       {
         calcMan.workerComplete(this);
-        if (guiProgress != null && progressId!=-1)
+        if (guiProgress != null && progressId != -1)
         {
           guiProgress.setProgressBar("", progressId);
         }
         ap.paintAlignment(true);
       }
-      if (msg.length()>0)
+      if (msg.length() > 0)
       {
         // TODO: stash message somewhere in annotation or alignment view.
         // code below shows result in a text box popup
-        /* jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
-        cap.setText(msg.toString());
-        jalview.gui.Desktop.addInternalFrame(cap, "Job Status for "+getServiceActionText(), 600, 400); */
+        /*
+         * jalview.gui.CutAndPasteTransfer cap = new
+         * jalview.gui.CutAndPasteTransfer(); cap.setText(msg.toString());
+         * jalview.gui.Desktop.addInternalFrame(cap,
+         * "Job Status for "+getServiceActionText(), 600, 400);
+         */
       }
     }
 
@@ -352,8 +356,11 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
   protected boolean bySequence = false;
 
   Map<String, SequenceI> seqNames;
+
   boolean[] gapMap;
+
   int realw;
+
   public List<FastaSequence> getInputSequences(AlignmentI alignment)
   {
     if (alignment == null || alignment.getWidth() <= 0
@@ -372,7 +379,7 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
     {
       seqNames = new HashMap<String, SequenceI>();
     }
-    gapMap=new boolean[0];
+    gapMap = new boolean[0];
     for (SequenceI sq : ((List<SequenceI>) alignment.getSequences()))
     {
       if (sq.getEnd() - sq.getStart() > minlen - 1)
@@ -386,25 +393,28 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
         FastaSequence seq;
         if (submitGaps)
         {
-          seqs.add(seq = new compbio.data.sequence.FastaSequence(newname,sq.getSequenceAsString()));
-          if (gapMap==null || gapMap.length<seq.getSequence().length())
+          seqs.add(seq = new compbio.data.sequence.FastaSequence(newname,
+                  sq.getSequenceAsString()));
+          if (gapMap == null || gapMap.length < seq.getSequence().length())
           {
-            boolean[] tg=gapMap;
-            gapMap=new boolean[seq.getLength()];
+            boolean[] tg = gapMap;
+            gapMap = new boolean[seq.getLength()];
             System.arraycopy(tg, 0, gapMap, 0, tg.length);
-            for (int p=tg.length;p<gapMap.length;p++)
+            for (int p = tg.length; p < gapMap.length; p++)
             {
-              gapMap[p]=false; // init as a gap
+              gapMap[p] = false; // init as a gap
             }
           }
-          for (int apos:sq.gapMap()) {
-            gapMap[apos]=true; // aligned.
+          for (int apos : sq.gapMap())
+          {
+            gapMap[apos] = true; // aligned.
           }
-        } else {
-        seqs.add(seq = new compbio.data.sequence.FastaSequence(newname,
-                AlignSeq
-                        .extractGaps(jalview.util.Comparison.GapChars,
-                                sq.getSequenceAsString())));
+        }
+        else
+        {
+          seqs.add(seq = new compbio.data.sequence.FastaSequence(newname,
+                  AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
+                          sq.getSequenceAsString())));
         }
         if (seq.getSequence().length() > ln)
         {
@@ -415,7 +425,7 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
     if (alignedSeqs && submitGaps)
     {
       realw = 0;
-      for (int i=0;i<gapMap.length;i++)
+      for (int i = 0; i < gapMap.length; i++)
       {
         if (gapMap[i])
         {
@@ -430,21 +440,24 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
         FastaSequence sq = seqs.get(p);
         int l = sq.getSequence().length();
         // strip gapped columns
-        char[] padded = new char[realw],orig=sq.getSequence().toCharArray();
-        for (int i=0,pp=0;i<realw; pp++)
+        char[] padded = new char[realw], orig = sq.getSequence()
+                .toCharArray();
+        for (int i = 0, pp = 0; i < realw; pp++)
         {
           if (gapMap[pp])
           {
-            if (orig.length>pp)
+            if (orig.length > pp)
             {
-              padded[i++]=orig[pp];
-            } else {
-              padded[i++]='-';
-            }       
+              padded[i++] = orig[pp];
+            }
+            else
+            {
+              padded[i++] = '-';
+            }
           }
         }
         seqs.set(p, new compbio.data.sequence.FastaSequence(sq.getId(),
-                  new String(padded)));
+                new String(padded)));
       }
     }
     return seqs;
@@ -452,7 +465,7 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
 
   /**
    * notify manager that we have started, and wait for a free calculation slot
-   *
+   * 
    * @return true if slot is obtained and work still valid, false if another
    *         thread has done our work for us.
    */