From: kiramt <k.mourao@dundee.ac.uk>
Date: Tue, 6 Jun 2017 14:56:04 +0000 (+0100)
Subject: JAL-2591 Removed getHiddenRegions()==null checks which are always false
X-Git-Tag: Release_2_10_3b1~183^2~17
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=0af3213cac54f10113b6fa2cbfb4523dae61b5b7;p=jalview.git

JAL-2591 Removed getHiddenRegions()==null checks which are always false
---

diff --git a/src/jalview/appletgui/AnnotationColumnChooser.java b/src/jalview/appletgui/AnnotationColumnChooser.java
index 60775d3..0a4748c 100644
--- a/src/jalview/appletgui/AnnotationColumnChooser.java
+++ b/src/jalview/appletgui/AnnotationColumnChooser.java
@@ -142,7 +142,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     }
     setOldHiddenColumns(av.getAlignment().getHiddenColumns());
     adjusting = true;
-    Vector<String> list = new Vector<String>();
+    Vector<String> list = new Vector<>();
     int index = 1;
     for (int i = 0; i < anns.length; i++)
     {
@@ -298,7 +298,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
         HiddenColumns oldHidden = av
                 .getAnnotationColumnSelectionState()
                 .getOldHiddenColumns();
-        if (oldHidden != null && oldHidden.getHiddenRegions() != null
+        if (oldHidden != null
                 && !oldHidden.getHiddenRegions().isEmpty())
         {
           for (Iterator<int[]> itr = oldHidden.getHiddenRegions()
diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 4aa205e..a72bbaa 100644
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -937,7 +937,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
   List<SequenceFeature> findFeaturesAtRes(SequenceI sequence, int res)
   {
-    List<SequenceFeature> result = new ArrayList<SequenceFeature>();
+    List<SequenceFeature> result = new ArrayList<>();
     SequenceFeature[] features = sequence.getSequenceFeatures();
     if (features != null)
     {
@@ -1501,7 +1501,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         {
           if (links == null)
           {
-            links = new Vector<String>();
+            links = new Vector<>();
           }
           for (int j = 0; j < sf.links.size(); j++)
           {
@@ -1926,8 +1926,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
     if (copycolsel
             && av.hasHiddenColumns()
-            && (av.getColumnSelection() == null || av.getAlignment()
-                    .getHiddenColumns().getHiddenRegions() == null))
+            && (av.getColumnSelection() == null))
     {
       System.err.println("Bad things");
     }
diff --git a/src/jalview/gui/AnnotationColumnChooser.java b/src/jalview/gui/AnnotationColumnChooser.java
index 9c2a1b9..5122f29 100644
--- a/src/jalview/gui/AnnotationColumnChooser.java
+++ b/src/jalview/gui/AnnotationColumnChooser.java
@@ -244,7 +244,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
         HiddenColumns oldHidden = av
                 .getAnnotationColumnSelectionState()
                 .getOldHiddenColumns();
-        if (oldHidden != null && oldHidden.getHiddenRegions() != null
+        if (oldHidden != null
                 && !oldHidden.getHiddenRegions().isEmpty())
         {
           for (Iterator<int[]> itr = oldHidden.getHiddenRegions()
@@ -727,7 +727,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
     private static final String FILTER_BY_ANN_CACHE_KEY = "CACHE.SELECT_FILTER_BY_ANNOT";
 
-    public JvCacheableInputBox<String> searchBox = new JvCacheableInputBox<String>(
+    public JvCacheableInputBox<String> searchBox = new JvCacheableInputBox<>(
             FILTER_BY_ANN_CACHE_KEY);
 
     public SearchPanel(AnnotationColumnChooser aColChooser)
diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index dee921e..1675bf0 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -180,13 +180,13 @@ public class Jalview2XML
    * Map of reconstructed AlignFrame objects that appear to have come from
    * SplitFrame objects (have a dna/protein complement view).
    */
-  private Map<Viewport, AlignFrame> splitFrameCandidates = new HashMap<Viewport, AlignFrame>();
+  private Map<Viewport, AlignFrame> splitFrameCandidates = new HashMap<>();
 
   /*
    * Map from displayed rna structure models to their saved session state jar
    * entry names
    */
-  private Map<RnaModel, String> rnaSessions = new HashMap<RnaModel, String>();
+  private Map<RnaModel, String> rnaSessions = new HashMap<>();
 
   /**
    * create/return unique hash string for sq
@@ -247,19 +247,19 @@ public class Jalview2XML
   {
     if (seqsToIds == null)
     {
-      seqsToIds = new IdentityHashMap<SequenceI, String>();
+      seqsToIds = new IdentityHashMap<>();
     }
     if (seqRefIds == null)
     {
-      seqRefIds = new HashMap<String, SequenceI>();
+      seqRefIds = new HashMap<>();
     }
     if (incompleteSeqs == null)
     {
-      incompleteSeqs = new HashMap<String, SequenceI>();
+      incompleteSeqs = new HashMap<>();
     }
     if (frefedSequence == null)
     {
-      frefedSequence = new ArrayList<SeqFref>();
+      frefedSequence = new ArrayList<>();
     }
   }
 
@@ -458,9 +458,9 @@ public class Jalview2XML
    * This maintains a map of viewports, the key being the seqSetId. Important to
    * set historyItem and redoList for multiple views
    */
-  Map<String, AlignViewport> viewportsAdded = new HashMap<String, AlignViewport>();
+  Map<String, AlignViewport> viewportsAdded = new HashMap<>();
 
-  Map<String, AlignmentAnnotation> annotationIds = new HashMap<String, AlignmentAnnotation>();
+  Map<String, AlignmentAnnotation> annotationIds = new HashMap<>();
 
   String uniqueSetSuffix = "";
 
@@ -536,7 +536,7 @@ public class Jalview2XML
    */
   private void saveAllFrames(List<AlignFrame> frames, JarOutputStream jout)
   {
-    Hashtable<String, AlignFrame> dsses = new Hashtable<String, AlignFrame>();
+    Hashtable<String, AlignFrame> dsses = new Hashtable<>();
 
     /*
      * ensure cached data is clear before starting
@@ -551,8 +551,8 @@ public class Jalview2XML
       // NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
       // //////////////////////////////////////////////////
 
-      List<String> shortNames = new ArrayList<String>();
-      List<String> viewIds = new ArrayList<String>();
+      List<String> shortNames = new ArrayList<>();
+      List<String> viewIds = new ArrayList<>();
 
       // REVERSE ORDER
       for (int i = frames.size() - 1; i > -1; i--)
@@ -662,7 +662,7 @@ public class Jalview2XML
     {
       FileOutputStream fos = new FileOutputStream(jarFile);
       JarOutputStream jout = new JarOutputStream(fos);
-      List<AlignFrame> frames = new ArrayList<AlignFrame>();
+      List<AlignFrame> frames = new ArrayList<>();
 
       // resolve splitframes
       if (af.getViewport().getCodingComplement() != null)
@@ -748,12 +748,12 @@ public class Jalview2XML
   {
     if (viewIds == null)
     {
-      viewIds = new ArrayList<String>();
+      viewIds = new ArrayList<>();
     }
 
     initSeqRefs();
 
-    List<UserColourScheme> userColours = new ArrayList<UserColourScheme>();
+    List<UserColourScheme> userColours = new ArrayList<>();
 
     AlignViewport av = ap.av;
     ViewportRanges vpRanges = av.getRanges();
@@ -807,9 +807,9 @@ public class Jalview2XML
     }
 
     JSeq jseq;
-    Set<String> calcIdSet = new HashSet<String>();
+    Set<String> calcIdSet = new HashSet<>();
     // record the set of vamsas sequence XML POJO we create.
-    HashMap<String, Sequence> vamsasSetIds = new HashMap<String, Sequence>();
+    HashMap<String, Sequence> vamsasSetIds = new HashMap<>();
     // SAVE SEQUENCES
     for (final SequenceI jds : rjal.getSequences())
     {
@@ -986,7 +986,7 @@ public class Jalview2XML
             pdb.setFile(matchedFile); // entry.getFile());
             if (pdbfiles == null)
             {
-              pdbfiles = new ArrayList<String>();
+              pdbfiles = new ArrayList<>();
             }
 
             if (!pdbfiles.contains(pdbId))
@@ -1135,7 +1135,7 @@ public class Jalview2XML
     /**
      * store forward refs from an annotationRow to any groups
      */
-    IdentityHashMap<SequenceGroup, String> groupRefs = new IdentityHashMap<SequenceGroup, String>();
+    IdentityHashMap<SequenceGroup, String> groupRefs = new IdentityHashMap<>();
     if (storeDS)
     {
       for (SequenceI sq : jal.getSequences())
@@ -1349,7 +1349,7 @@ public class Jalview2XML
                 .getFeatureRenderer().getRenderOrder()
                 .toArray(new String[0]);
 
-        Vector<String> settingsAdded = new Vector<String>();
+        Vector<String> settingsAdded = new Vector<>();
         if (renderOrder != null)
         {
           for (String featureType : renderOrder)
@@ -1392,7 +1392,7 @@ public class Jalview2XML
         // is groups actually supposed to be a map here ?
         Iterator<String> en = ap.getSeqPanel().seqCanvas
                 .getFeatureRenderer().getFeatureGroups().iterator();
-        Vector<String> groupsAdded = new Vector<String>();
+        Vector<String> groupsAdded = new Vector<>();
         while (en.hasNext())
         {
           String grp = en.next();
@@ -1415,7 +1415,7 @@ public class Jalview2XML
       {
         jalview.datamodel.HiddenColumns hidden = av.getAlignment()
                 .getHiddenColumns();
-        if (hidden == null || hidden.getHiddenRegions() == null)
+        if (hidden == null)
         {
           warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
         }
@@ -2290,7 +2290,7 @@ public class Jalview2XML
     try
     {
       // create list to store references for any new Jmol viewers created
-      newStructureViewers = new Vector<JalviewStructureDisplayI>();
+      newStructureViewers = new Vector<>();
       // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
       // Workaround is to make sure caller implements the JarInputStreamProvider
       // interface
@@ -2383,8 +2383,8 @@ public class Jalview2XML
       initSeqRefs();
     }
     AlignFrame af = null, _af = null;
-    IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<AlignmentI, AlignmentI>();
-    Map<String, AlignFrame> gatherToThisFrame = new HashMap<String, AlignFrame>();
+    IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<>();
+    Map<String, AlignFrame> gatherToThisFrame = new HashMap<>();
     final String file = jprovider.getFilename();
     try
     {
@@ -2525,9 +2525,9 @@ public class Jalview2XML
    */
   protected void restoreSplitFrames()
   {
-    List<SplitFrame> gatherTo = new ArrayList<SplitFrame>();
-    List<AlignFrame> addedToSplitFrames = new ArrayList<AlignFrame>();
-    Map<String, AlignFrame> dna = new HashMap<String, AlignFrame>();
+    List<SplitFrame> gatherTo = new ArrayList<>();
+    List<AlignFrame> addedToSplitFrames = new ArrayList<>();
+    Map<String, AlignFrame> dna = new HashMap<>();
 
     /*
      * Identify the DNA alignments
@@ -2669,7 +2669,7 @@ public class Jalview2XML
     errorMessage = null;
   }
 
-  Map<String, String> alreadyLoadedPDB = new HashMap<String, String>();
+  Map<String, String> alreadyLoadedPDB = new HashMap<>();
 
   /**
    * when set, local views will be updated from view stored in JalviewXML
@@ -2840,7 +2840,7 @@ public class Jalview2XML
 
     List<SequenceI> hiddenSeqs = null;
 
-    List<SequenceI> tmpseqs = new ArrayList<SequenceI>();
+    List<SequenceI> tmpseqs = new ArrayList<>();
 
     boolean multipleView = false;
     SequenceI referenceseqForView = null;
@@ -2908,7 +2908,7 @@ public class Jalview2XML
       {
         if (hiddenSeqs == null)
         {
-          hiddenSeqs = new ArrayList<SequenceI>();
+          hiddenSeqs = new ArrayList<>();
         }
 
         hiddenSeqs.add(tmpSeq);
@@ -3116,12 +3116,12 @@ public class Jalview2XML
 
     // ////////////////////////////////
     // LOAD ANNOTATIONS
-    List<JvAnnotRow> autoAlan = new ArrayList<JvAnnotRow>();
+    List<JvAnnotRow> autoAlan = new ArrayList<>();
 
     /*
      * store any annotations which forward reference a group's ID
      */
-    Map<String, List<AlignmentAnnotation>> groupAnnotRefs = new Hashtable<String, List<AlignmentAnnotation>>();
+    Map<String, List<AlignmentAnnotation>> groupAnnotRefs = new Hashtable<>();
 
     if (vamsasSet.getAnnotationCount() > 0)
     {
@@ -3276,7 +3276,7 @@ public class Jalview2XML
                   .get(an[i].getGroupRef());
           if (aal == null)
           {
-            aal = new ArrayList<jalview.datamodel.AlignmentAnnotation>();
+            aal = new ArrayList<>();
             groupAnnotRefs.put(an[i].getGroupRef(), aal);
           }
           aal.add(jaa);
@@ -3366,7 +3366,7 @@ public class Jalview2XML
         }
         int pidThreshold = jGroup.getPidThreshold();
 
-        Vector<SequenceI> seqs = new Vector<SequenceI>();
+        Vector<SequenceI> seqs = new Vector<>();
 
         for (int s = 0; s < jGroup.getSeqCount(); s++)
         {
@@ -3759,7 +3759,7 @@ public class Jalview2XML
      * Run through all PDB ids on the alignment, and collect mappings between
      * distinct view ids and all sequences referring to that view.
      */
-    Map<String, StructureViewerModel> structureViewers = new LinkedHashMap<String, StructureViewerModel>();
+    Map<String, StructureViewerModel> structureViewers = new LinkedHashMap<>();
 
     for (int i = 0; i < jseqs.length; i++)
     {
@@ -3957,8 +3957,8 @@ public class Jalview2XML
 
     Set<Entry<File, StructureData>> fileData = data.getFileData()
             .entrySet();
-    List<PDBEntry> pdbs = new ArrayList<PDBEntry>();
-    List<SequenceI[]> allseqs = new ArrayList<SequenceI[]>();
+    List<PDBEntry> pdbs = new ArrayList<>();
+    List<SequenceI[]> allseqs = new ArrayList<>();
     for (Entry<File, StructureData> pdb : fileData)
     {
       String filePath = pdb.getValue().getFilePath();
@@ -4014,9 +4014,9 @@ public class Jalview2XML
               getViewerJarEntryName(svattrib.getViewId()));
     }
 
-    List<String> pdbfilenames = new ArrayList<String>();
-    List<SequenceI[]> seqmaps = new ArrayList<SequenceI[]>();
-    List<String> pdbids = new ArrayList<String>();
+    List<String> pdbfilenames = new ArrayList<>();
+    List<SequenceI[]> seqmaps = new ArrayList<>();
+    List<String> pdbids = new ArrayList<>();
     StringBuilder newFileLoc = new StringBuilder(64);
     int cp = 0, ncp, ecp;
     Map<File, StructureData> oldFiles = svattrib.getFileData();
@@ -4577,8 +4577,8 @@ public class Jalview2XML
       af.viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
       String[] renderOrder = new String[jms.getFeatureSettings()
               .getSettingCount()];
-      Map<String, FeatureColourI> featureColours = new Hashtable<String, FeatureColourI>();
-      Map<String, Float> featureOrder = new Hashtable<String, Float>();
+      Map<String, FeatureColourI> featureColours = new Hashtable<>();
+      Map<String, Float> featureOrder = new Hashtable<>();
 
       for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
       {
@@ -4637,7 +4637,7 @@ public class Jalview2XML
           fdi.setVisible(setting.getType());
         }
       }
-      Map<String, Boolean> fgtable = new Hashtable<String, Boolean>();
+      Map<String, Boolean> fgtable = new Hashtable<>();
       for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
       {
         Group grp = jms.getFeatureSettings().getGroup(gs);
@@ -4830,7 +4830,7 @@ public class Jalview2XML
       String[] magicNames = new String[] { "Consensus", "Quality",
           "Conservation" };
       JvAnnotRow nullAnnot = new JvAnnotRow(-1, null);
-      Hashtable<String, JvAnnotRow> visan = new Hashtable<String, JvAnnotRow>();
+      Hashtable<String, JvAnnotRow> visan = new Hashtable<>();
       for (String nm : magicNames)
       {
         visan.put(nm, nullAnnot);
@@ -4842,11 +4842,11 @@ public class Jalview2XML
                         + auan.template.getCalcId()), auan);
       }
       int hSize = al.getAlignmentAnnotation().length;
-      List<JvAnnotRow> reorder = new ArrayList<JvAnnotRow>();
+      List<JvAnnotRow> reorder = new ArrayList<>();
       // 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<String>(visan.keySet());
+      List<String> remains = new ArrayList<>(visan.keySet());
       for (int h = 0; h < hSize; h++)
       {
         jalview.datamodel.AlignmentAnnotation jalan = al
@@ -5174,7 +5174,7 @@ public class Jalview2XML
   {
     if (datasetIds == null)
     {
-      datasetIds = new Hashtable<String, AlignmentI>();
+      datasetIds = new Hashtable<>();
       return null;
     }
     if (datasetIds.containsKey(datasetId))
@@ -5188,7 +5188,7 @@ public class Jalview2XML
   {
     if (datasetIds == null)
     {
-      datasetIds = new Hashtable<String, AlignmentI>();
+      datasetIds = new Hashtable<>();
     }
     datasetIds.put(datasetId, dataset);
   }
@@ -5211,7 +5211,7 @@ public class Jalview2XML
       // make a new datasetId and record it
       if (dataset2Ids == null)
       {
-        dataset2Ids = new IdentityHashMap<AlignmentI, String>();
+        dataset2Ids = new IdentityHashMap<>();
       }
       else
       {
@@ -5490,11 +5490,11 @@ public class Jalview2XML
         // register sequence object so the XML parser can recover it.
         if (seqRefIds == null)
         {
-          seqRefIds = new HashMap<String, SequenceI>();
+          seqRefIds = new HashMap<>();
         }
         if (seqsToIds == null)
         {
-          seqsToIds = new IdentityHashMap<SequenceI, String>();
+          seqsToIds = new IdentityHashMap<>();
         }
         seqRefIds.put(jv2vobj.get(jvobj).toString(), (SequenceI) jvobj);
         seqsToIds.put((SequenceI) jvobj, id);
diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index cb19539..8a24937 100755
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -403,20 +403,17 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
 
     res = av.getAlignment().getHiddenColumns().adjustForHiddenColumns(res);
 
-    if (av.getAlignment().getHiddenColumns().getHiddenRegions() != null)
+    for (int[] region : av.getAlignment().getHiddenColumns()
+            .getHiddenRegions())
     {
-      for (int[] region : av.getAlignment().getHiddenColumns()
-              .getHiddenRegions())
+      if (res + 1 == region[0] || res - 1 == region[1])
       {
-        if (res + 1 == region[0] || res - 1 == region[1])
-        {
-          reveal = region;
-          ToolTipManager.sharedInstance().registerComponent(this);
-          this.setToolTipText(MessageManager
-                  .getString("label.reveal_hidden_columns"));
-          repaint();
-          return;
-        }
+        reveal = region;
+        ToolTipManager.sharedInstance().registerComponent(this);
+        this.setToolTipText(
+                MessageManager.getString("label.reveal_hidden_columns"));
+        repaint();
+        return;
       }
     }
   }
@@ -499,7 +496,7 @@ public class ScalePanel extends JPanel implements MouseMotionListener,
       gg.setColor(Color.blue);
       int res;
 
-      if (av.getShowHiddenMarkers() && hidden.getHiddenRegions() != null)
+      if (av.getShowHiddenMarkers())
       {
         for (int i = 0; i < hidden.getHiddenRegions()
                 .size(); i++)
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index c6c2deb..7651eb4 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -2145,8 +2145,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     if (copycolsel
             && av.hasHiddenColumns()
-            && (av.getAlignment().getHiddenColumns() == null || av
-                    .getAlignment().getHiddenColumns().getHiddenRegions() == null))
+            && (av.getAlignment().getHiddenColumns() == null))
     {
       System.err.println("Bad things");
     }
diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 60cee46..107cdd4 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -1159,7 +1159,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   @Override
   public boolean hasHiddenColumns()
   {
-    return colSel != null
+    return alignment.getHiddenColumns() != null
             && alignment.getHiddenColumns().hasHiddenColumns();
   }