Adjustments according to review comments;

src/main/java/de/unijena/cheminf/mortar/controller/HistogramViewController.java

@@ -1126,11 +1126,11 @@ private Double[] calculateBarSpacing(int aNumberOfDisplayedFragments, BarWidthOp
         double tmpGapDeviation;
         double tmpGapSpacing;
         double tmpCategoryGap;
-        double tmpFinalHistogramHeight = 0;
+        double tmpFinalHistogramHeight = 0.0; //return value is initialised here with a default value
         double tmpFinalGapSpacing;
         switch (aBarWidthOptionConstant) {
             case SMALL:
-                if (aNumberOfDisplayedFragments <= 24) {
+                if (aNumberOfDisplayedFragments <= 24) { //magic number
                     tmpCurrentHistogramHeight = GuiDefinitions.GUI_NOT_SCROLLABLE_HEIGHT / aNumberOfDisplayedFragments;
                     tmpGapDeviation = tmpCurrentHistogramHeight / (GuiDefinitions.GUI_NOT_SCROLLABLE_HEIGHT / 24);
                     tmpGapSpacing = HistogramViewController.GUI_HISTOGRAM_SMALL_BAR_GAP_CONST * tmpGapDeviation;
@@ -1144,7 +1144,7 @@ private Double[] calculateBarSpacing(int aNumberOfDisplayedFragments, BarWidthOp
                 }
                 break;
             case MEDIUM:
-                if (aNumberOfDisplayedFragments <= 17) {
+                if (aNumberOfDisplayedFragments <= 17) { //magic number
                     tmpCurrentHistogramHeight = GuiDefinitions.GUI_NOT_SCROLLABLE_HEIGHT / aNumberOfDisplayedFragments;
                     tmpGapDeviation = tmpCurrentHistogramHeight / (GuiDefinitions.GUI_NOT_SCROLLABLE_HEIGHT / 17);
                     tmpGapSpacing = HistogramViewController.GUI_HISTOGRAM_MEDIUM_BAR_GAP_CONST * tmpGapDeviation;
@@ -1159,7 +1159,7 @@ private Double[] calculateBarSpacing(int aNumberOfDisplayedFragments, BarWidthOp
                 break;
             case LARGE:
             default:
-                if (aNumberOfDisplayedFragments <= 13) {
+                if (aNumberOfDisplayedFragments <= 13) { //magic number
                     tmpCurrentHistogramHeight = GuiDefinitions.GUI_NOT_SCROLLABLE_HEIGHT / aNumberOfDisplayedFragments;
                     tmpGapDeviation = tmpCurrentHistogramHeight / (GuiDefinitions.GUI_NOT_SCROLLABLE_HEIGHT / 13);
                     tmpGapSpacing = HistogramViewController.GUI_HISTOGRAM_LARGE_BAR_GAP_CONST * tmpGapDeviation;

src/main/java/de/unijena/cheminf/mortar/model/data/MoleculeDataModel.java

@@ -162,9 +162,7 @@ public IAtomContainer getAtomContainer() throws CDKException {
         try{
             tmpAtomContainer = ChemUtil.parseSmilesToAtomContainer(this.uniqueSmiles, true, true);
         } catch (CDKException aCdkException){
-            //TODO: log this? It blows up the log file quite a bit
-            //Logger.getLogger(MoleculeDataModel.class.getName()).log(Level.WARNING, "atom container parsed from SMILES "
-            //        + this.uniqueSmiles + " could not be kekulized or atom types assigned to it.", aCdkException);
+            //no logging, this happens too often, e.g. for fragments of aromatic rings
             tmpAtomContainer = ChemUtil.parseSmilesToAtomContainer(this.uniqueSmiles, false, false);
         }
         tmpAtomContainer.addProperties(this.properties);